Superheroes do fight bigoted villains, especially if they're X-Men, whose entire rogues gallery that isn't fellow mutants consists of bigots who want to annihilate them just for existing as mutants. That said, I do like your idea of superheroes taking a stand against institutionalized violence, even if that would jeopardize the surprisingly cozy relationships superheroes have tended to (sometimes) enjoy with elements of law enforcement and the military and/or government.