Hughie is the protagonist. The viewer and nearly every other character relate to him and his actions. Butcher OTOH is a violent inconsiderate weirdo who is hated by everyone, including his parents. (He is barely tolerated by those he has dragooned onto his "team".) Butcher was convenient for getting the action started but after he transitioned from "mysterious stranger" to "surrogate father" to "everyone hates this asshole", his role would have been better filled by others on the team.

It would be a considerably more "experimental" program if a character like Butcher were the actual protagonist.