People don't like to hear superior because of real life. But in real life we know that stereotypes aren't true Black people aren't more violent that other people and the black men all have don't monster size
, All Asians aren't smart, Some white people do have rhythm and can jump. Nothing than makes a person "better" in real life is tied to genetics(it is tied to hard work) in a form that would make some from a different race unable to match the feat. That is not true of mutants they simple are born better and Surge is way faster than Usain Bolt by virtue of being a mutant.Gentle was simple born a mutant and he is stronger than strongest human, Prodigy was just born a mutant and he is smarter than Reed.
Michael Jordan was greatest basketball players his sons weren't good at basketball, Michael jackson kids aren't amazing musicians,etc.
While mutants is literally someone genetics making them better in a way that can't be match by most if any of the human population. It is not "skill" it is their dna.
Because of comic book storytelling, It is not matter of mutants want their cake and eating it .It is that comic storytellers have run with a trope which never has made as much sense we think it does and until now many fans haven't faced reality what the X-men and mutants really are if they are organized together. But back to point Magneto ,Franklin, Legion or somebody would have taken over the world or part of the world and erase knowledge of mutants. And mutants would live in peace and that does not make for a good comic book. There is a reason the editors keep reducing the population of mutants in books because if the population gets high enough.There is really no reason to hate mutants in the manner being push in the narrative.
At least now the hate fear and narrative makes sense, Humans are now up against united group of people who are threat to destroy them all and some flaunting the fact the better than them. And possible war that could lead extinction of humans could happen(Irony of hating mutants forced them to unite so basically humans forced they feared into reality). Yeah mutant hate makes sense now. Humans have always bullied mutants because they weren't unified, Now mutants are in position to where they can bully the humans back and that has never happened before because they wanted the X-men to be underdog minority metaphor. In comic world were they aren't trying to push a hate and fear narrative people with Metagene aka X-gene aren't universal hated like we see DC comics(Heck most superpower beings have the metagene in DC). Narrative go can many directions depending on the creator.