While I see your point, and I'm not at all painting you with this brush, I think that reasoning could also be used to argue that, e.g., autistic people are lesser beings. I know it's a different universe, but look at Superman: Unquestionably a superior being, but like Professor X, he never put himself on that pedestal. Magneto's insistence that non-mutants are and maybe should be subservient pretty much requires conflict, and starts folks down a path towards subjugation, enslavement, and ultimately elimination. Note: not extinction. Elimination requires action, while extinction, allowing for mitigating circumstances, does not.
Add to all of this that it's pretty easy to understand, and even relate to the origins of how Magnet and Professor X see non-mutants, and X-Men is a pretty great story/universe. They're both similarly flawed, but in very different ways.