Well in the beginning of the X-Men in the 60s you turned on the news and saw the kkk who still had political power in the south and Midwest and white citizens council protesting anything integration related riots and the like
So it wasn’t that hard to say "people cant get along with other skin colors let alone superpowers ….Now the x-men means any thing that’s oppressed because its “different”
And all I need to know about how stupid people get about things like that is go on face book ……… its just exaggerated in the comics
In the 60s, when the comic started, it was really more like Cold War-era paranoia - you didn’t know who was a mutant/commie, and the concern was more that they were running things secretly using mind control or other sinister powers (which, actually, Professor X was quite prone to do). The most unusual looking mutants when things started were a fat guy (the Blob) and a squat ugly guy (the Frog). Beast was the freakiest mutant and that was only because he experimented on his own DNA.
It wasn’t until the Claremont era that we got the weirder-looking mutants like Mystique and Nightcrawler and leaned into the prejudice/civil rights analogs. Sure, the original team tried that narrative, but since they were essentially five somewhat rich white kids being mentored by an even richer white guy, the title never got much traction with that.