Magneto's problem isn't that he uses "evil methods" - an enemy that actively genocides your people with giant murder robots cannot be opposed peacefully. if you do that, the giant murder robots just go and genocide you. Magneto's mistake is not that he fights for mutant liberation with violent means (in fact, the X-Men use violent methods themselves when it's necessary, they even threaten and blackmail the president in one of the movies), but rather that he has internalized the suprematist logic of his persecutors and merely inverted it. Lacking a truly liberatory ideological framework, Magneto has chosen to become the oppressor himself and replace human suprematism with mutant suprematism.

there's still a bunch of problems with that. when we make that an analogy of real-world problems (and the x-men are frequently seen as that, with mutants having been coded as a stand-in for all kinds of minorities from black people to jews to LGBTs). this is dangerously close to become an accusation of "inverse racism" or "homosexism" or a comparable reactionary strawman. at best, magneto's story as a holocaust survivor who wants to create a safe mutant state to prevent his people from genocide, but then ends up with a suprematist system of oppression and apartheid could be viewed as a critique of zionism, but that analogy is awfully problematic as well because then the group that's the stand-in for jews is opposed to humans, which is :yikes: af because it implies that the jews in this analogy are not human beings.

so i'd say that Magneto is always kind of a problematic figure, but he has the potential to be an interesting, complex villain, he has the potential to pose an actual moral dilemma and it's usually not as much of a simple, clearcut case as in other late-capitalist media where "let's improve society somewhat" is simply equated with murdering puppies.