The play Waiting for Godot is a representative of the theater of the absurd, which is a movement that is borne from the philosophy of existentialism. If you take a close look, the subtitle of the play is "A tragi-comedy in two acts." Hence this is one of the points that tells us that the play will show pieces of satire and sadness in one same plot.
Moreover, the characters of Godot do show a sense of satire for common situations. There is plenty of black humor to support the argument that it could very well be an existentialist way to mock life. The black humor comes from the fact that the play aims to make jokes of moments of intense pain.
An example of this black-humored mockery is the relationship between Pozzo and Lucky. This is mockery because it satirizes the oppression of the upper classes against the destitute. It mocks it further giving the unhappy, hopeless man in the duo the ironic name of "Lucky". Additionally, the way in which Lucky is inhumanely treated produces a movement of the scene that makes the characters sloppy, blunt, and silly. This is a type of vaudeville humor as well.
Another example is the conditions that the characters suffer. Estragon is spaced-out, forget full, has smelly feet, and is a mocked as a simpleton. Vladimir has kidney problems, bad breath, and is over sensitive. Pozzo is extremely cruel and abusive, but his abusive techniques are somewhat funny in that they are pointless. Lucky is just a poor soul that depends on Pozzo for subsistence. But every time he is asked to entertain and we picture him dancing at Pozzo's command it is hard not to laugh. This is how this humor is considered "dark", or "black"- because it is creepy and subtle.
Concisely, you can conclude that Waiting for Godot, as a tragi-comedy, will show episodes of mockery in the form of black humor and satire. Therefore, it does mock the main characters because this is another way to mock the trivialities of life and society.