There are no specific quotes in this play that show Doctor Faustus to be an atheist. He rather choses to ignore the reality of God instead of consciously not believing in God in the first place. In his opening soliloquy in Act I scene 1, for example, he turns his attention to Biblical theology, and writes it off as meaningless and fatalistic before turning to his magic books with great excitement and hope:

The reward of sin is death? That’s hard.
Si peccasse negamus, fallimur, et nulla est in nobis veritas.
If we say that we have no sin,
We deceive ourselves, and there’s no truth in us.
Why then belike we must sin,
And so consequently die.
Ay, we must die an everlasting death.
What doctrine call you this? Che sarà, sarà:
What will be, shall be! Divinity, adieu!
These metaphysics of magicians,
And necromantic books are heavenly!

Here, Marlow turns to the Bible and reads out quotes from the books of Romans and John: "The reward of sin is death" and "If we say we have no sin/we deceive ourselves, and there's no truth in us." Faustus thinks that as it is impossible not to sin, Christianity only offers nothing more than a secure death based in our innate sinfulness. As a result, he bids "adiue" to "Divinity," as he argues that such a creed offers no hope to humans. The way he turns instead to his "metaphysics" and "necromantic books," describing them blasphemously as "heavenly" on the other hand, clearly reveals where his loyalties lie. In this quote, Faustus attempts to write off Christianity and the existence of God as being illogical, and thus this would be a good quote to use in discussing his beliefs about religion and God. The irony is of course that the second quote from the Bible goes on to talk about repentance; something that Faustus systematically ignores until it is too late.