I'm going to deal with a different direction to answer your question about writing a thesis concerning Waiting for Godot. The previous answer deals with the philosophical aspects of your question. I'll deal with the practical. I think maybe you are at least partly asking for help writing the thesis statement itself, so I'll try to help you with that.
You will need to review the play with the subversion of capitalist ideology in mind. You need to gather evidence for the text that demonstrates what exactly is being revealed about capitalist ideology. Once you have this evidence, analyze and categorize it, lump everything together that demonstrates the same main point. Once you decide what can be proven, you can write a thesis.
Your thesis can deal with whatever you decide on:
- how theme contributes to the subversion
- how dialogue is used to contribute to the subversion
- how the absurd situation contributes...
- how a certain scene ...
You can use whatever you discover as the thesis for your essay. A sample:
In Beckett's Waiting for Godot, the capitalist ideology is subverted by....
I'm not writing that any of the above will necessarily work for your essay, I'm just giving examples of how to go about arriving at your thesis.
My initial reaction to the thesis statement is that it is a very interesting application of Beckett's work, but might not be capturing the full essence of its intent. Certainly, Beckett is making a strong statement about the nature of capitalist pursuits. In this mindset, the character of "Godot" would be the acquisition of material wealth and the desire to accrue more capital. This would be the notion of waiting for "Godot," as there is always more wealth to be obtained and more of its trappings which provide allure. The "waiting" would be to presume that capitalism can provide something related to substantive meaning to consciousness. Certainly, one could make this argument. However, I think Beckett was himself and in his work elusive enough to not capitulate to the idea that a statement of anti- capitalism can translate into another vision of totality. There is a definite undermining of all totalizing visions in the work, as each notion of totality and transcendence can be seen as a form of "waiting." Capitalism, socialism, or any other notion of the good which professes to be "the answer" is severely undermined with the nature of Beckett's work. With this in mind, I think that the thesis is quite meaningful, in so far as it makes clear that the work might be subversion to any notion of the transcendent good.
Beckett's whole body of work especially Godot and Endgame are often considered to be texts that depict the alienation of the capitalist subject. Adorno's article on Endgame is a case in point. Beckett's inversion of all possible ideologies (all ideologies are dictatorial, as it were) in the semantic dead ends and neutralizations in the play are evocative of a subversion of capitalism. The stress on the de-classed and renegadede category of the tramp, the parody of pedagogy and all forms of imposed truths, the continually reversible master-slave relation of Lucky and Pozzo which does not posit the Hegelian master-slave dialectic but rather shows its loop-holes---all these are inroads into the work, as far as the given theme is concerned.
Brecht had even sketched a socialist version of this play in his last years. His death made the production a Godot like absence, for which we still wait, only in vain.