In the prologue of The Jew of Malta, he says, "I count religion but a childish toy." Does he mean that religion is a childish toy, or is he saying that religion is anything but a childish toy?
This line comes form the Prologue, spoken by Machiavel, that is, the Florentine political philosopher Machiavelli, a symbol of unrestrained immorality in the Elizabethan period:
I count religion but a childish toy,
And hold there is no sin but ignorance.
Birds of the air will tell of murders past!
I am asham'd to hear such fooleries.
The second line makes it clear that Machiavel...
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I suspect Marlowe is having this fictional character (the "ghost of Machiavel" - a fairly straightforward link to the real Machiavelli) mock religion as a thing suited only to children's minds; he goes on to suggest that "ignorance" is the problem for adult minds.
The audience might not take this character's views too seriously (it was a deeply religious time) but Marlowe would still have managed to plant negative ideas about religion here. Although this play is a fiction, in real life, Marlowe seems to have questioned supernatural ideas and included religion in these.