I gotta run counter to the many people who agree with magneto and say the mutant registration advocates. XD (except trask. fuck that guy.)
Your parallel to the gay rights/ civil rights movement kind of breaks down when you try to compare the relatively harmless state of being gay/a different race to having superpowers that can potentially break the universe. For a long time, characters who championed mutant registration only wanted that: to keep track of what mutants could do, because if a guy can melt brains by looking at you funny, you deserve to know about it. It's draconian, but in a unique situation like that it's a fairly measured response.
Writers eventually realized the portrayal was a bit uneven, and started making the anti-mutant side a lot more conventionally evil, wanting to deport/isolate mutants if not destroy them outright, at which point my agreeing with them ended, but for a while I could see where they were coming from.
On the video games side... hmm, he probably doesn't count as a villain, since you get negative karma for killing him, but he can stand against you in game. Mr. House from Fallout: New Vegas. no matter what you said about him, you couldn't really deny his love of new vegas and desire to see humanity recover were both genuine.