Did Christopher Marlowe, who received a Parker scholarship for divinity students and knew the Bible through and through, transform from a Church-of-England Protestant to an atheist by 1593? So some of his contemporaries would have us believe. Was Shakespeare, who knew the Bible like the back of his hand, a conforming Protestant, a closet Catholic, or an atheist? All three possibilities have been advanced. I think it more likely that in “both” cases, Marlowe and the Bard were free thinkers who sometimes chafed against the Church of England’s stranglehold on religion.
Let us start with Marlowe. I will discuss him not in relation to the accusations of atheism flung about during his day, but in terms of what, in my view, his dramas tell us. His early plays show the dire consequences for those who are irreligious. In II Tamburlaine, Tamburlaine burns the Koran and blasphemes against the prophet Mahomet, “whom I have thought a god” (V.i.175). Tamburlaine says that there is a vengeful God, whose scourge he is, and he will obey God only, then dares Mahomet to come down from heaven and work a miracle. Sixty lines later Tamburlaine has taken ill, and then dies.
In Doctor Faustus, the protagonist famously sells his soul to the devil. The demon Mephistopheles tries to talk him out of it:
Think’st thou that I, who saw the face of God
And tasted the eternal joys of heaven,
Am not tormented with ten thousand hells
In being deprived of everlasting bliss?
O Faustus, leave these frivolous demands,
Which strikes a terror to my fainting soul! (Sc. iv.79-84)
In his blinding hubris, Doctor Faustus signs away his soul, then fritters away his twenty-four years of life with supernatural powers, achieving nothing of consequence. Devils carry off the man, now full of regret, to hell at the end of the play.
Doctor Faustus has long been a controversial play, subject to various interpretations. I favor the viewpoint of scholars who detect in the play a critique of the Calvinist doctrine of predestination which, although hotly debated during Marlowe’s time, had come to be the Church of England’s position: God preordains eternal life for some, and damnation for others, and man has no control over his ultimate fate. At the beginning of the play, Faustus reads Romans 6:23, which he translates from the Latin as: “The reward of sin is death,” and adds, “That’s hard” (Sc. 1.41). He then quotes 1 John 1:8: “If we say that we have no sin,/ We deceive ourselves, and there’s not truth in us” (Sc. 1.44-5). He notes, “Why then belike we must sin” and terms this doctrine, “What will be shall be.” Here is the predestination and resultant despair about which anti-Calvinists complained. Is it really the case that all men are sinners, and nothing that a person does can affect the decision God has already made about whether any given individual will enter heaven? Indeed, this is it not the full story, Biblically speaking. Faustus does not go on to cite the very next line of 1 John, 1:9: “If we confess our sins, he is faithful and just to forgive us our sins, and to cleanse us from all unrighteousness.”
Throughout the play, the Good Angel appears. He tells Faustus that contrition, repentance and prayer can bring him to heaven. God will pity him, and it is “never too late.” The Good Angel appears one last time (1616 Text) shortly before the devils arrive to bring Faustus to Hell, and tells Faustus that if only he had listened to him, he would have received innumerable joys. Here Marlowe’s stance follows Jesus’ parable of the prodigal son: the Father will rejoice and accept back into His home a sinner who repents. In my view, Doctor Faustus is assuredly not the work of an atheist, but rather of a man who thought for himself and questioned church doctrine. It was the work of a man who believed in a more enlightened approach to forgiveness than was common in his day.
In his play Edward II, Marlowe employs irony when those who oppose each other in warfare invoke God for their cause, one after the other. The Earl of Kent pronounces, “Rain showers of vengeance on my cursèd head,/ Thou God, to whom in justice it belongs/ To punish this unnatural revolt!” (Sc. xix.7-9). Yet immediately afterwards, Queen Isabel, who has unnaturally revolted against her husband, enters and says, “Successful battles gives the God of kings/ To them that fight in right and fear his wrath./ Since then successfully we have prevailed,/ Thanks be heaven’s great architect” (Sc. xix.19-22). Is God supposed to support one side, both, or neither in crushing its enemies? Later on, though, just before King Edward’s murder, he cries out, “Assist me, sweet God, and receive my soul!” His poignant cry contains not a hint of irony.
Marlowe’s The Jew of Malta shines a spotlight on the religious hypocrisy of both Christians and Jews. Marlowe does not criticize the religious tenets themselves, but rather the fact that people who profess to hold them lay them aside and behave abominably when it suits their purposes. The Turks come to Malta to claim their ten years’ tribute, but the Christian Knights of Malta have spent the money on warfare. The Knights impose a fine of half the Jews’ estates in order to pay the money due to the Turks, and at the same time do not fine Christians. Barabas retorts, “Will you then steal my goods?/ Is theft the grounds of your religion?” (I.ii.95-6).
The governor of Malta notes Barabas’ “inherent sin,” i.e., as Christians saw it, the Biblical justification for anti-Semeticism: that the blood of Christ was on the hands of the Jews who demanded that Jesus be crucified, and their descendants (Matthew 27:25). Barabas responds, “What? Bring you scripture to confirm your wrongs? Preach me not out of my possessions.” The governor piously replies, “Excess of wealth is cause of covetousness, and covetousness, O, ‘tis a monstrous sin,” to which the Jew says, “Ay, but theft is worse” (I.ii.111-2, 124-6). Any sympathy the audience may feel for Barabas is, however, quickly turned to disgust as he manipulates his innocent daughter and the man she loves into becoming instruments of his revenge.
Shakespeare follows a similar arc in The Merchant of Venice, which echoes The Jew of Malta’s “Bring you scripture to confirm your wrongs?” above, with “The devil can cite Scripture for his purpose” (I.iii.97). Shylock the Jew complains, “O father Abram, what these Christians are,/ Whose own hard dealings teaches them suspect/ The thoughts of others” (II.ii.159-60). Shylock gains sympathy with his “If you prick us do we not bleed?” speech, and antipathy for his plan to extract a pound of flesh from Bassanio, who owes him money.
Bassanio, too, spotlights religious hypocrisy:
So may the outward shows be least themselves.
The world is still deceived with ornament.
What damnèd error but some sober brow
Will bless it and approve it with a text,
Hiding the grossness with fair ornament? (III.ii.73-4, 77-80)
Both The Jew of Malta and The Merchant of Venice use a play about a Jew to question the two-facedness of some Christians, while at the same time telling a story about good vs. evil where, on Renaissance England stages, audiences expect the Jew to represent evil.
In Shakespeare works, as Gary Sloane noted, prayers “are often a prelude to disaster.”  In Titus Andronicus, Titus, who has chopped off one hand to ransom the lives of two sons, prays, "O, here I lift one hand up to heaven/ And bow this feeble ruin to the earth./ If any power pities wretched tears,/ To that I call" (III.i.205-8). A messenger then enters with his two sons’ heads. In King Lear, when Albany learns that Edmund has ordered the death of Cordelia, he says, “The gods defend her!” (V.iii.252). Immediately afterwards, Lear enters, holding Cordelia’s dead body. The most pious of Shakespeare’s monarchs, Henry VI, is also the weakest. Although the historical King Henry VI was both pious and weak, the Bard doesn’t sugarcoat him.
As Marlowe questioned the Church of England’s stance in Doctor Faustus, so too did Shakespeare in The Comedy of Errors. According to Donna B. Hamilton’s insightful interpretation, the play parodied how the Church of England treated nonconformists such as Puritans and separatists.  The play’s religious orientation is signaled by its location, not in Epidamnum, the setting of its source, the Menaechmi by Plautus, but rather in Epheseus. St. Paul’s Epistle to the Ephesians emphasizes hierarchical relationships between master and servant and mother and wife. In Acts of the Apostles, evil spirits abound in Epheseus, reminding us of how Dr. Pinch is called to excise spirits in The Comedy of Errors.
The Comedy of Errors contains two sets of identical twin brothers, the two twins named Antipholus, one of Epheseus and the other of Syracuse, and the two Dromios, one from each town. This is one more set of twins than in its source.
The Puritans called each other brother, a salutation that future Archbiship of Canterbury Richard Bancroft found divisive. According to Hamilton:
Shakespeare reconstituted the contested term ‘brother’ so that the emphasis is not on divisiveness or difference, but on difference (Syracusan and Ephesian) that is ultimately subsumed and overridden by sameness. In this case, brotherhood is not a problem, but the solution. Everything can come out all right, the audience is made to understand, as soon as someone—in this case, it will be the Abbess—finally realises that, different though they may be, they are all of one family. 
Until they make that realization, though, people suffer. Egeon is to be executed at sundown. The servant Dromios are arbitrarily hit and beaten. This symbolizes the violence nonconformists experience at the hands of the ecclesiastical court system. It is the violence that would Marlowe would have experienced had he not “died.”
Because Adriana thinks her husband has been unfaithful, she locks him out of the house, analogous to how the Church and the Queen of England locked out noncomformists whom it viewed as unfaithful. Her mistaken belief that he has been disloyal is caused by her own confusion. Indeed, Luciana tells Antipholus of Syracus that he should pretend to be faithful to his wife, even if he is not: “Or if you like elsewhere, do it by stealth” (III.ii.7). The analogy is to nonconformists having to attend Church of England services and outwardly conform, while maintaining other practices and beliefs in private. Moreover, Protestants portrayed the Catholic Church as the Whore of Babylon, and both conformist and nonconformist Protestants falsely denounced each other as papists. These charges are symbolized by Adriana accusing Antipholus of Epheseus of consorting with a courtesan, and Antipholus of Epheseus accusing Adriana of being a dissembling harlot.
When the Abbess, who is not in the source, gives Antipholus and Dromio of Syracuse sanctuary, she offers a unifying alternative to the Church of England: stop locking people out, and let them in. The final lines say it all. The twin Dromios discuss who should enter the priory first. Dromio of Epheseus says, “We came into the world like brother and brother,/ And now let’s go hand in hand, not one before the other” (V.i.429-30).
Hamilton also compared Shakespeare’s King John with the earlier, anonymous play it was drawn from, The Troublesome Raigne of King John. In revising the earlier play, the Bard replaced one set of values with another. The Troublesome Raigne is stridently anti-Catholic, and shows officials interrogating someone until he admits a private matter which will shift fortunes when made public. King John removes the strident tone, and portrays private conversation about private matters as the norm. The previous decade, Archbishop Whitgift had implemented the controversial ex officio mero oath, whereby the accused had to vow to answer all questions put to him by the ecclesiastical court before knowing what those questions would be, leading to forced self-accusation. Lord Burghley compared the procedure to Spanish Inquisitors trapping their prey. The Bard subtly positions his play in opposition to ex officio.
He also positions King John on the side of power grounded in law, jure humano, as opposed to power emanating from an authority higher than a human power, jure divino; his message is that ecclesiastic courts ought not to usurp powers that ran contrary to common law. Hamilton concluded:
In King John, Shakespeare presents himself and the English people as loyal and obedient subjects, but also as subjects who, like [James] Morice, are able to make distinctions between that which is just and that which is not, between that which is hurtful and that which is not. 
Why actor, landowner and grain hoarder William Shakspere from Statford-upon-Avon concerned himself with matters of church and state is unclear. Why Marlowe would have done so is obvious. In my view, the overweening power of the church cost him his identity, and could have cost him his life, had he not faked his own death.
Without preaching religion, Shakespeare plays affirm core values common to the world’s religions, such as mercy, love and forgiveness. Yet because they do not advocate one religion, instructors in secular schools the world over can teach Shakespeare’s works. Thank God that the Bard took a more enlightened approach than the leaders of the Church of England during the Renaissance.
By Donna N. Murphy, 2015. All rights reserved.