If I was a mutant then pro mutant. If I was not then anti-mutant. The reasoning is relatively simple: violence between the two sides is absolutely inevitable. If I am not a mutant then letting people walk around possessing weapons of mass destruction is against my best interests. If I am a mutant, then I'd probably not want to be subjugated by an inferior iteration of humanity on the basis that I might do something.
As a result neither side in the X-men seems like they can be called "right". To argue that a man like Charles Xavier ought to be allowed to act freely on the basis that he hasn't done anything wrong is folly because one cannot wager humanity itself on nothing more than the fact he hasn't done anything yet. Giving one man the literal power to enslave the world if he so chose (and he's just one mutant with the power to sweep aside all human achievements on a whim - there are others) is absolutely foolish if you have any stake in that world. By contrast, while pragmatic considerations would argue against such people, basic morality stand on their side. Given that I'd have to advocate what amounts to vast invasion of privacy and almost certainly genocide to protect humanity there is no way to argue that I've made the morally correct choice. Necessity and morality thus stand at intersection and the only deciding factor is who's corpses would be used to build the new world.
As a result neither side in the X-men seems like they can be called "right". To argue that a man like Charles Xavier ought to be allowed to act freely on the basis that he hasn't done anything wrong is folly because one cannot wager humanity itself on nothing more than the fact he hasn't done anything yet. Giving one man the literal power to enslave the world if he so chose (and he's just one mutant with the power to sweep aside all human achievements on a whim - there are others) is absolutely foolish if you have any stake in that world. By contrast, while pragmatic considerations would argue against such people, basic morality stand on their side. Given that I'd have to advocate what amounts to vast invasion of privacy and almost certainly genocide to protect humanity there is no way to argue that I've made the morally correct choice. Necessity and morality thus stand at intersection and the only deciding factor is who's corpses would be used to build the new world.