he wrote this play. One writer explains that Godot may refer in some sense to "God," while...

Less Francophile readings have insisted it should scan as 'Go.dot', a reference to the mental and physical movement that must result from Existential inertia.

In this case, "God" is completely lost, and this reference would signify that there is no place in the play for "God." However, it is ironic to note that Beckett was (strangely) suspicious of words—that they could not be controlled... implying that Beckett had a desire to do just that (and what his audience thought along with that, perhaps).

[Beckett] eventually dismissed language itself as a reliable source of security. Ironically, this man of words ultimately mistrusted them. He knew that the word could never be counted on to convey meaning precisely and that linguistic meaning was always an approximation.

One of the "natural beauties" of literature (thank God...or Godot...?) is that no one can control what a reader thinks. In a search for understanding of Beckett's puzzling play, we are able to decide whether God is there or not. The eNotes summary on themes in the play states:

[Vladimir and Estragon] live without amenities, find joy in the smallest of victories, and are ultimately quite serious about their vague responsibility to wait for this mysterious figure who may or may not come...

Perhaps the sadness of the story, which can be as true for you and I as readers, as Beckett's perceptions were to him, is that God was there all the time—they just never noticed Him. The "smallest victories" the men experience in their desolation may be God's way of trying to speak to them, but they listen instead to the hopeless words of Pozzo:

The tears of the world are a constant quantity. For each one who begins to weep, somewhere else another stops.

When Pozzo and Lucky leave, a boy arrives and says that Godot won't come today, but will tomorrow. The men continue into the second act, doing much the same as they had in the first: waiting. Pozzo and Lucky return: Pozzo is blind and Lucky is mute. And still nothing changes for Vladimir and Estragon. After all this time has passed, the boy arrives again and tells them they must wait until tomorrow for Godot.

Is the boy symbolic of an angel? Is he telling them that God will not be there that day because the men do not believe? Is the boy, however, offering hope that they can find God tomorrow if they wish to?

Beckett may have believed there was no God, but he cannot control how an audience perceives his play. He may want the reader to believe that the waiting of the men is pointless and that God is an illusion. However, it is quite possible to believe that the illusion is simply that there is nothing around them in the first place. Sometimes we sit and fail to notice our surroundings. All of a sudden a bird's call or the buzzing of a bee may attract our attention to what is right there in front of us: the miraculous palette of nature's colors and creations.

Vladimir and Estragon don't find God, but it may be from the lack of trying: for failing to open their eyes and see him in the smallest things, believing the pessimistic ravings of Pozzo, and the foolishness of Lucky (while he may still speak).

Sources:

http://www.spikemagazine.com/0896name.php

http://www.enotes.com/waiting-for-godot/themes

http://www.enotes.com/waiting-for-godot/summary