OG Magneto's outlook on humanity and the future of mutants was founded on past experiences in his life. But he was also very abusive, megalomaniacal and domineering to other mutants and also wanted to conquer the world in his own image. So while his past is tragic, ultimately hes still a villain whos plans for both mankind and mutants needed to be stopped. In the one timeline where Magnus took over the world, you still had class division and castes of mutants above other mutants, so the problem doesn't really fucking fix itself. Even if you restrict it to the movies themselves, Magneto thinks of lesser mutants not in his inner-circle as pawns. Hes completely willing to kill a mutant child and Wolverine. Magneto at his best shouldn't be some martyr figure who can completely deconstruct humanity, because thats just fundamentally ignoring the laundry list of war crimes and personal faults.