VLADIMIR
(stopping) Your turn.
Estragon does the tree, staggers.
ESTRAGON
Do you think God sees me?
VLADIMIR
You must close your eyes.
Estragon closes his eyes, staggers worse.
ESTRAGON
(stopping, brandishing his fists, at the top of his voice.) God have pity on me!
VLADIMIR
(vexed) And me?
ESTRAGON
On me! On me! Pity! On me!
Enter Pozzo and Lucky. Pozzo is blind. Lucky burdened as before. (2.451-6)
Notice that Pozzo enters as an answer to Estragon’s plea for pity, making a mockery of Gogo’s idea of a "savior." The help sent to him is a blind tyrant and his slave, which actually isn’t so helpful. Also note that Estragon is pretending to be a tree when he asks Vladimir if God can see him; we describe the tree’s religious significance in "Symbolism, Imagery, and Allegory" if you’re interested, but the quick explanation is that tree = cross (as in, the crucifixion kind).
Quote 53
VLADIMIR
(He looks again at Estragon.) At me too someone is looking, of me too someone is saying, He is sleeping, he knows nothing, let him sleep on. (2.795)
As Vladimir looks at the sleeping Estragon, he remarks that someone else is watching him (Vladimir) sleep. The "someone else" is presumably God, which in this comparison puts Vladimir in a deity-like position over Estragon.
Quote 54
VLADIMIR
(softly) Has he a beard, Mr. Godot?
BOY
Yes Sir.
VLADIMIR
Fair or . . . (he hesitates) . . . or black?
BOY
I think it's white, Sir.
Silence.
VLADIMIR
Christ have mercy on us! (2.823-27)
Vladimir puts two and two together here and concludes that Godot is God. This would be completely logical, except he’s basing his logic on a speech given by a ranting slave tied up on a rope, commanded to think by a tyrannical, deity-like figure, and able to do so only with the help of a bowler hat. The reason his final line in this quote is so emotional is that he fears the consequences of missing a meeting with Godot—even moreso than before.