theres a bunch of reasons to hate mutants , and it goes well beyond "you fear what you dont understand"
for most of humankind, it comes down to this a$$hole
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he declared war on humankind before they were aware of what mutants were.
has done shyt like emp'd the world, took nukes and aimed them at countries, dropped a satellite in orbit causing massive weather fluctuations, as well as being head of the brotherhood of evil mutants.
and his overall arrogance.... jesus.
thats not to say that humans havent done terrible shyt in turn though. the sentinels have wrought destruction on mutantkind in insane ways
then you have psychics. number 2 problem with mutant perception. the very definition of all the power, none of the responsibility
and those are just the times theyve used their powers on friends and allies. theres a reason magneto is smart enough to wear that damn helmet all the time.
another has to do with the xmen in general. theyve gone back and forth with having villains on and off teams that most people at this point just assume that the xmen are just down with the fukked up shyt that villainous mutants do
the fukked up part is that because of that, the real losers in all this are mutants with no powers because the ones withh powers flex so hard that the hate trickles down
another reason is the randomness of what a mutant means. being a mutant is a literal crapshoot. someone can manifest the power to control butterflies, someone else can threw shards of glass from their hands, and someone on the extreme end can produce a gas from their body that kills people within a certain distance you dont know what your getting, even with parents with particular powers.