There probably is an angle where you could make mutants a threat. For most normal people living in the MCU these super heroes are only seen on TV. You would see big battles in New York, Sokovia etc. but most people wouldn't think these could happen in your back yard and you would never see Iron Man or Thor flying overhead causing havoc. If suddenly there is a mutation where your friends or family could have superpowers then suddenly all the destruction seen on peoples TV would suddenly feel a lot closer to home.