Maybe it's all Magneto's fault!
I remember that way, way back in "Uncanny X-Men #150" (published in the early 1980s), Storm said to Magneto,
with considerable justice, "If we are hated and feared, it is in large part because of you!"
I believe he was the first high-profile self-declared "mutant" to deliberately do things that would garner lots of headlines in the Silver Age comics, and he quickly formed a villainous group with the catchy name of "The Brotherhood of
Evil Mutants." That may have strongly shaped the initial public perception of what sort of people "mutants" really are.
Just think -- on the theory I'm developing, it seems
probable that if Storm had simply spent her entire career introducing herself to people in terms of "I'm a weather-controlling
witch" instead of "I'm a weather-controlling
mutant," perhaps she would have become the darling of American liberals who felt absolutely obligated to prove that they were
not prejudiced against a person who was a) black, b) female, c) confident and powerful, and d) claimed her powers had something to do with "the traditional magic" of her African ancestors.
But Ororo Munroe made one fatal mistake -- she frequently used the word "mutant" to describe herself, and that made
all the difference!