Religion is incompatible with reason in Waiting for Godot. Characters who attempt to understand religion logically are left in the dark, and the system is compared to such absurd banalities as switching bowler hats or taking a boot on and off. Religion is also tied to uncertainty, since there is no way of knowing what is objectively true in the realm of faith.
Waiting for Godot operates on one damning, principal contradiction: the men can only be saved if their personal god, Godot, were to appear. However, since a commonly accepted interpretation of God is that he is without extension (meaning he doesn’t occupy space), Godot’s presence would mean that he is not God. This renders Vladimir and Estragon’s waiting absurdly futile.