This article nicely summarizes the prejudice faced by non-religious people and tries to explain why it happens:
So why are atheists “among the least liked people … in most of the world,” in the words of a research team led by University of British Columbia psychologist Will Gervais? In a newly published paper, he and his colleagues provide evidence supporting a plausible explanation.
Atheists, they argue, are widely viewed as people you cannot trust.
“People use cues of religiosity as a signal for trustworthiness,” the researchers write in the Journal of Personality and Social Psychology. Given that “trustworthiness is the most valued trait in other people,” this mental equation engenders a decidedly negative attitude toward nonbelievers.
Not an easy problem to solve.