Magneto is one of my favorite characters... he's a great villain with a lot of scope and a tremendously imposing power-set which makes him a valid threat without being unbeatable. He's probably the best major villain in that regard, since Doom is mostly Mary Sue'd with plot powers. Secret Wars summed it up Magneto best, imo. He was placed on the "heroes" team because his desires weren't selfish but that doesn't mean he's not a villain. There's another great scene where Captain America says he doesn't trust Magneto and Magneto snaps at him and argues that Captain America, the least bigotted person in the Marvel Universe, is jealous/afraid of him and doesn't trust him because he's a mutant. Completely overlooks the real reasons Captain America would have for not trusting him to instead preach his own tirade about how mutantshe is oppressed and unfairly treated.
When it comes down to it, Magneto is a nasty spiteful man. He is a bully with a superiority complex that he hides behind what appears to be valid justification for his actions. The classic case of the bullied become the bullies. But as we've seen countless times, when it comes down to it, Magneto's superiority isn't based on him being a mutant but rather him feeling he is better than everyone else. A great example of this is in Planet X (oh, wait, no because it's Grant Morrison so naturally it's all retconned away) but you have Magneto as much as abusing socially and mentally challenged students into serving his will while only faux humoring them. There really isn't a better scene to summarize Magneto than the bit where Esme and Toad are insulting and acting superior to the "Special Class" and Magneto tells them off for doing so with his falsely indignant attitude - happy to ignore the fact that he himself is abusing the children himself. Only heightened by the fact that he drops his whole righteous façade countless times and displays his own belief of personal superiority when they Special Class interrupt him, annoy him, question him, etc. And just because Marvel spared no quarter to retcon the whole story, it doesn't mean that it's not valid Magneto characterisation. It was written and printed as such, so shut up.
If Magneto ever gets his way or wins, he's still a nasty person who believes himself better than everyone else. I mean, even Bendis recognized this for god's sake (probably by accident).
The nonsense "hero" Magneto is just offensively stupid. He's a bully. Just because the current stable of writers are too dimwitted to appreciate the complexities of the character, they just go off of like a one sentence summary of the character. Same with Doom. Neither of these mega-villains are noble, they only believe themselves to be such. They see themselves as misunderstood and noble because actions and circumstance have twisted them that way, but it doesn't mean they are misunderstood and noble.
Headmaster Magneto worked because it was exploring the idea of Magneto teaching the next generation and adopting a slightly different approach. He was still a villain through-and-through, just not active as such. He was happy to find an opportunity to blame humans for the troubles which plagued mutantshimself and whenever the New Mutants wouldn't listen to him he would snap at them and using his authoritative position over them to exert his own superiority. While you can say he did some "heroic" things during this period, this is also the period where he refused to help his "friends" the X-Men battle the Adversary because they were risking their lives for humanity in doing so and was really gunning to twist the New Mutants to his own agenda.
This is from Mark Millar's Ultimate X-Men run (where Magneto is consistently written great btw), but I think it's a really really good scene showing Magneto's "noble heroism":
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