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You’re getting a lot of answers that are more sympathetic to Magneto than he deserves.
I’d argue that Magneto has a slightly better argument on diagnosing the problem (that humans and mutants can’t peacefully coexist) than Professor X (that humans and mutants must find a way to peacefully coexist).
But the logical diagnosis of “the humans will genocide the mutants of we let them” doesn’t make Magneto the good guy when he prescribes a solution for that problem. The history of the character oscillates between trying to create segregated societies where mutants are separate and not accountable to the human world, or outright subjugation or genocide of the humans.
Maybe peaceful coexistence isn’t possible. But is it better to continually strive for that ideal, or is it better to reject humanity entirely and create strict segregation (or destruction) of the other side?