Atheists aren't really the most-hated or most-despised group in America because they suffer so few hate crimes. If they aren't being killed or beaten for being atheists, they must not be as hated as those who are.
We probably can't know for sure how many hate crimes atheists might experience because of the consequences which people might suffer from admitting their atheism atheists are in the same position as gays not too long ago. That said, however, it is likely that atheists don't experience as many hate crimes as Jews, blacks, and other minorities. Doesn't this mean that atheists aren't as disliked? No, because it misrepresents what is being stated in saying that atheists are the most hated.
A great many people hate to varying degrees, but few people will assault or even kill others because of their hate. To commit such crimes requires a great deal more hate, but it's not a hate that many people have. A thousand hate crimes might be committed by one or two hundred people and if they were the only people who hated, that's a relatively small amount of intense hatred.
When atheists say that they are the most hated and most despised group in America, it doesn't mean that the hatred of atheists is the most intense and strongest of any hatred. What it means is that hatred and distrust of atheists is far more widespread, prevalent, and even socially acceptable as compared to the hatred of any other group in America.
The hatred some people have of blacks or Jews may be intense enough to inspire crimes, but the number of people who hate that much is much smaller than the number of people who are willing to express hatred of atheists. Even the number of people who are willing to admit to distrusting and disliking Jews or blacks is far lower than those willing to admit to distrusting and disliking atheists.
Atheists are certainly fortunate that they aren't so intensely hated that they have to actively fear being assaulted or killed because of their atheism, but they do have to fear discrimination on the job, in the community, and even in their own families if their atheism is made known. Some even have to contend with harassment and vandalism. Distrust and hatred of atheists is widespread enough through American society that atheist have plenty of reasons to be concerned.
Some theists use the above myth to dismiss or minimize the widespread hatred of atheists. Given the prevalence of Christianity in America, it only follows that most of those who hate, distrust, and are willing to discriminate against atheists are "good Christians" who promote their religion as a force for peace. The fact that there are fewer people whose hatred of atheists is as intense as the small number who hate Jews and blacks enough to assault them doesn't justify the above claim, however.
Religious theists in America, and especially Christians, are simply going to have to come to terms with the fact that their religion may use "peace" and "love" a lot in its theological rhetoric, but this rhetoric doesn't always translate into real behavior. Some people are simply too different to love and treat as full equals. Atheists fall into this category for a large number of religious believers and Christians in America.