As the title of the book indicates, Billy is our main focus, the hero of our tale. The narrator makes it very clear that the story was written to remember Billy and to set the record straight about what happened to him. We are concerned with Billy's failure to respond to the afterguardsman's threat of mutiny, and later with whether or not he can be condemned for killing John Claggart.
It is worth noting, however, that the narrator repeatedly stresses how simple and innocent Billy is. Since the protagonist is generally the person at the center of the action, with whom we are most sympathetic, this raises a question about what it means to be a protagonist in the case of Billy Budd. A lot of things happen to Billy, but he doesn't do much to actually bring anything about. If we're concerned with agency, with the person who causes things to happen and has control over them, then we should look to Captain Vere, not Billy Budd.