Well, let's just be up front about it and say that these labels don't really fit. There isn't exactly a "bad guy" in Endgame, but Clov isn't quite Hamm's companion either. But, if we're playing the game and we've labeled Hamm the protagonist, then that makes the guy that he bickers with the antagonist. Much of the tension of the play comes from the master-servant relationship between Hamm and Clov. Clov constantly questions Hamm's authority and acts defiant in all sorts of small ways, but he never completely undermines him. Clov allows Hamm to be the protagonist, but he is also threatening to Hamm because Hamm is completely dependent on him.
Zooming out for a hot second, let's consider the conflict of the play: are they going to give up and accept defeat or are they going to carry on? Here, Clov again contrasts Hamm because he is very much ready for things to end, while Hamm constantly wants them to keep on playing. Which, in this play, is roughly the same thing as living.