It might be hard to think of Cory as an antagonist, since he's pretty much the nicest guy ever. For most of the play, he puts up with his grouchy father, Troy, without too much of a fuss. Chances are the audience is really rooting for him to get to go to college on the football scholarship. Chances are the audience is heartbroken when Troy squashes his dreams. In a lot of plays, this would make Cory the protagonist, but not in Fences.
Though Cory is a nice guy, he doesn't cause anything to happen; that's Troy's job in this play. The father/son battle at the climax is revealing. When you see the protagonist of a play fighting someone near the end, there's a high probability that that person is the antagonist. In this case, our protagonist, Troy, dukes it out and defeats none other than his son, Cory. This climactic battle makes it pretty clear that Fences has a case of one of the most likable antagonists ever.