This article is from the X-Men Comic Books FAQ, by Kate the Short (email@example.com) with numerous contributions by others.
Andrew Ingle supports an interesting theory, one that works inside the
Marvel Universe: "The people love superheroes. They dress up in spandex
and save the world! They're celebrities to them, brilliant, beautiful
celebrities. And you can see Cap or someone when they're coming. You
KNOW they're Cap. Their powers are their powers and that's what lets
them protect the world. They get their abilities for a reason. However,
a mutant is someone born with their powers, and they DON'T always dress
up in Spandex and advertise it. When you walk down the street, you don't
know whether the person across the crosswalk will spontaneously shoot
you with poisonous acid blasts from his eyeballs. Anyone can be a
mutant, but only Johnny Storm is The Human Torch. The fact that mutants
can be anyone is what scares people."
As for the plots, Peter Lidkis reminds us, "There is hatred for mutants
in the MU. The difference is that Avengers is not THE book that focuses
on it. It only occassionally looks in on that hatred and then goes on
its next story line." So it's not unusual for people to overall love
the Avengers or FF--they're not *meant* to be hated as a matter of
course. The X-Men were meant to deal with prejudice and hate, so they're
going to end up being hated.