An idea for why mutants are hated in the MCU --------------------
"Mutants" and evolution and "change" should be a big deal going forward in the MCU, but primarily told via the mutant-based movies. What makes the possibility of mutants seem scary isn't the fact that they are born with abilities. (Because otherwise, people would fear the Avengers) It's because of how the government will use propaganda to make society scared of people born with abilities, because the government will not be able to control nor keep quiet their continuing population increase (This is where the social commentary would come into play) Politicians for example trying to make people paranoid about who could be a mutant. The fear is that they will outnumber normal humans eventually; that'd be the spin and the truth. Make people scared of them so that the government can legally track them, and eventually legally contain them, or legally kill them. All of which they'd already be doing, but without legislation. That's where the the Mutant Registration Act comes into play -- which should be brought up at the end of the movie. The X-Men are rarely ever appreciated by the Government. So after they save the day, they are not rewarded with applause like the Avengers were in TA. They are rewarded with seeing a news conference of the Government announcing new legislation that will lead to further persecution of mutants.
What do you guys think?