Magneto’s mutant pride attitude is in every way more admirable than Xavier’s preference for the closet, and Xavier’s political view that mutants and humans can coexist peacefully if mutants avoid provocations is directly contradicted by the events at the end of the film. When Xavier is trying to convince Magneto (and the audience) that Magneto’s more militant methods will cost innocent life he literally says—to a Holocaust survivor!—that “they were only following orders” and therefore their sins are forgivable.
Not surprisingly I don't really agree with this analysis. I see the point he is trying to make and it is an allowable reading of the movie, but it misses out on the methods that Magneto wants to use to meet his end of Mutant Pride and his mistaken view of what it means to be human.
The mutant pride message is a radical one. It’s too radical for those whose WASP male privilege in their non-mutant lives makes them instinctively want to identify with existing power structures. But a mutant who’s also a Jew, or a woman, or a racial minority, or has had blue or red skin all of his or her life doesn’t suffer from that kind of false consciousness and gets ahead of the curve.
The problem is that for Magneto, mutant is a separate species and category than human. He's not addressing the issue as a minority normally would be, "I am part of society and am fully human." Instead Magneto argues that mutants are beyond super human, are a new species, and thus should dominate the world. Sure Xavier is naive, but he wants to see the humanness in mutants and wants humans to see mutants as humans. I don't know why that's a bad thing.