The X-men type mutants had powers that seemed to defy the known laws of physics. But, they showed pretty often that most mutants had more drawbacks than benefits.

What made Magneto a villain was that he decided that mutants were the next evolutionary step, and that humans were therefore obsolete. It wasn't even like predicting that mutants were superior and that as a result eventually humans would fade away. It was that he decided that one "race" was superior and therefore was justified in ruling over the inferior race. Which, you know, is pretty dark for a holocaust survivor.