We say everybody believes they're in the right. That's probably true, but some people do things terrible enough that they OUGHT to know they're not. Hitler, for example. Probably should have known he wasn't on the proverbial side of the angels.
Yes, Magneto has done evil things and should be held accountable for them. But I think (when written by Claremont or other more sympathetic writers, anyway) he's one of the villains who HONESTLY, as opposed to delusionally, sees himself as being in the right. And I think that counts for something.