Some writers (like Busiek) have done a good job of explaining it. Otherwise, it's just another example of different character setups ruffling each other a bit in an expanded universe (similar to a world that is simultaneously meant to be very much like our own in the grittier street-level books and housing people like Reed Richards and Hank Pym). It's easy to see why people would be worried about a race of new people growing up to supplant humanity; mutants are (or were) the most pervasive example of that, whereas random freaks are just that (and it's not like all heroes get a great reception; Spider-Man, for example).