Mutants are not superior. They just think they are. And that is problematic. As others have said, there are people who can run faster than you, who are smarter than you are, who can lift more weight than you can, who are better looking than you are, but that does not make them superior to you. Mutant powers do not make mutants superior to anyone on planet [Marvel] earth. If they're resistant to diseases, that does not make them superior. The only valid excuse mutants have for isolating/self-segregating themselves--and they are using it to the hilt--is victimhood. And fans are buying into the mutant whine fest (for 616), too.
If mutants are so superior, than why are they always victims of the "inferior" humans? They want their cake and they want to eat it too--we're superior and we're victims. The two beliefs of superiority and victimhood is exactly how white nationalists and Neo Nazis rationalize their violent plans for the rest of us "inferiors" who don't measure up.
In the evolutionary sense, mutants are not superior either. Evolution is about survival in a changing environment, and passing ones genes on to future generations. It takes place over thousands and millions of years. On Marvel earth, one could argue that the Mole Men are superior to everyone because they mind their own business, live underground, and once the mutant supremacists and human supremacists finish destroying one another, the Mole Men will be the only survivors.
Mr. Sinister probably was the first to come with the pseudo-scientific term "Homo Superior." Moira and Charles came across the term at Oxford (where Essex was a disguised professor) and Charlie passed it on to Magnus in Israel, where Magnus once he became Magneto, ran with it. So does the current Cerebro-head Xavier actually believe mutants are superior, or that they need to have a place to live on earth in peace? Because Xavier, for all his flaws, never believed that mutants were "superior" to anyone but that great powers gave them great responsibility towards those not so endowed as themselves. Which in a meta sense, is Marvel's philosophy.
Because someone is stronger than you are, doesn't make them superior to you. It means they have a different set of skills than you do. If they choose to use their different talents, greater strength, greater charisma and social skills--or super powers--in order to take what they want and destroy what stands in their way, it's called being an evil assh*ole. Not the next step in evolution. If a group of people, a cult, a "religion" like the one L. Remini has exposed (I'm almost afraid to name them) thinks they're "superior" and too good to live among lesser beings and they isolate themselves with strict hierarchies and bizarre organizational charts, wonky belief systems that tell followers they will never die and they'll always be resurrected, etc., I call that a scam that supports the status and power of the few at the top who are instituting and controlling the community.