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.
I guess the issue here is about how you are defining ‘superior.’ If the argument is that mutants are in some way morally or ethically superior to non-mutants, absolutely not. And that is the source of a lot of the conflict in the comics. But in terms of what they can actually achieve in life, when you can do something like Magento does, you’ve got an inherent superiority.
Now I admit that you can’t make that claim for all mutants. Not even all X-Men. I would not say that Cyclops’ mutant power makes him an inherently superior human in terms of power because it severely limits him in many other ways and, if he wasn’t on a team that regularly needed his power, would find life pretty difficult.
So I guess you can’t argue that all mutants are superior, but many of the ones we see could basically rule all of humanity if they were allowed to get away with it.
Even Cyclops is inherently superior, from looking at capability. So you really think any human, any police force even, can stand against him?
Yes. Take him by surprise and he’s as easy to kill as anyone else, and he has no powers that make him more aware than an average human.
Magneto’s insistence that non-mutants are and maybe should be subservient
Magneto is a prime example of “might makes right”, which is why he’s a villain. Non-mutants are beneath him: he has no compassion for them, no regard for their ideas, their voice, their opinion.
I’m not well versed in his history in the comics or whether there even is a canonical backstory, but from the Marvel perspective …… he’s a sympathetic villain, because he has a good point. While it’s not a single coherent backstory, we can see his development over time at the treatment he faced, and can have sympathy for humanity driving him to it.