Didn't mutant hysteria die downed already, I remember it did when it was peaked in the mid-80s in Dazzler outing and then the X-men sacifice in Dallas on live television got people thinking of the x-men as heroes and X-factor who revealed that they scam everyone got a ticket parade after saving New york from Apocalypse. It would be logical progression, I guess the legacy virus report by Trish Tribly got people scared again.
I guess it also has to do with the X-Men ways of doing things as the animated series put it with Gambit with Beast. "We seem to be more fighting for our lives than for mutant rights."
There were rare examples of the X-men doing the right thing and confronting racisim like in God loves, Man kills when they confronted Styker and ended up with him looking bad by try to shoot Kitty(ended beign save by a cop, one of the few good ones, wish Spidey had cop friends like that rather than the douchebags that framed him for making them look bad) or when Kitty, Illyana and Collossus confronted a mob in the first issue of Mutant Massacre who were about to jump on a injured Kurt.