OP, the point, you are missing it.
Mutants do not exist in a bubble. They exist in a Marvel universe, where superpowers (not mutants!), magic, techno-viruses, Gods (hell, pantheons of gods), demonic realms, GODS with all capitals, Higher beings, ALIENS are all a regular form of threat to earth.
In this mix, focusing on mutants due to human insecurity IS horrible. Absolutely horrible.
If it is power you fear, humans have other worries: see the post about the leaders one button push away from a nuclear apocalypse.
If you do not have sympathy for the X-Men who were persecuted, attacked and/or killed while they were regularly saving the world, then I do not know what to say. It is like you agree with shooting a medic in the head while he is working on a patient because he do not have a VISA or has a high debt to your country's bank. BULLSHIT!
An argument can be made that mutants, at minimum, have the same rights as humans. That is the minimum. An argument can be made that they actually have more, if we really want to go the way the humans have treated all species on earth so far (i.e. if it is inferior to us, we can openly abuse it, cage it, vivisect it, torture it, consume it), and I suppose that is the real source of fear that humans might have when mutants appear. i.e. the fear that they would recieve the same treatment as THEY would give to their inferiors if they were in such positions.
It is the same argument as the one where someone wants to shoot the aliens down if they see one because "they obviously want to conquer us/wage war against us", or as others argued, if they have higher tech, they would obviously just nuke our planet. I.e.: That is what humans would do if we would get the ability to go to other planets. Enslave, destroy, fuck, eat.
So....it is a complicated issue, and if someone would be in need of getting no sympathy for me, it is the makers of Sentinels, Trask and Co, and the marauders.