The Washington Post published an essay titled Why do Americans still dislike Atheists? which doesn’t really address that question but does point out that atheists are smarter, richer, and just plain cooler than believers. Which is probably also why we’re disliked — atheists tend to be insufferable with all the science and reason talk (though to be fair I have known plenty of racist, homophobic, Glenn Beck-watching atheists too).
I’m not so sure I’m buying the claims by Gregory Paul and Phil Zuckerman about how cool atheists are (this is another problem with atheist — we’re all a bunch of pedantics). For example, Paul and Zuckerman note that many Americans seem to view atheists as amoral or immoral but,
Consider that at the societal level, murder rates are far lower in secularized nations such as Japan or Sweden than they are in the much more religious United States, which also has a much greater portion of its population in prison. Even within this country, those states with the highest levels of church attendance, such as Louisiana and Mississippi, have significantly higher murder rates than far less religious states such as Vermont and Oregon.
There are a lot of reasons the U.S. has higher murder rates than secular European and Asian states, but I doubt religiosity is a major reason. If Paul and Zuckerman just want to claim that, see, Europeans don’t go around on murderous rampages and they’re much more secular than U.S., fine, but I call confounding factors on that comparison and the Louisana/Mississippi comparison.
Similarly, the United States has a huge percentage of its population in prison largely because of the War on Drugs. Depending on the study, about a quarter of all jail inmates and more than half of all federal prisoners are incarcerated for drug-related crimes.