What are your thoughts on Mutants as an analogue for persecuted minorities in our own society? I can see some parallels, but there is no race, creed, or sexual orientation with members who can read minds, manipulate metal, create illusions, walk through solid objects, etc. It’s hard not to sympathize with people who see Mutants as potentially dangerous.

See here and here. 

At the same time, I don’t think that “mutants are dangerous” is a good counter-argument; show me a persecuted minority that wasn’t believed to be dangerous to the majority or to have unnatural abilities. The fact that mutants exaggerate the historical rhetoric doesn’t make it a good argument. 

Mutants exist in a world in which Galactus and Mephisto are real; the fact that public policy focuses on the “mutant threat” is ultimately due to feelings of inadequacy, of being an evolutionary dead end, not a clear-eyed risk assessment. Hence the constant use of the scientifically-incorrent Neanderthal metaphor: