I think the fact that you choose not to read what people are actually posting, instead projecting some sort of false cause onto other people so you can feel better about yourself, illustrates a far more serious problem in "this" country (I assume by "this country" you mean "this planet" because there are literally no modern social issues you can apply to the United States alone).
Religion serves two primary psychological functions: first, and foremost, it is a background for community-building. The people who attend the same church, or even follow the same religion, share a common bond which helps smooth out social organization. When I have children they are going to attend church every sunday even though I strongly disapprove of organized religion, because I believe forming these peaceful social bonds is critical in a healthy person's development (as opposed to the sort of social organizations that are built up in a school yard, which are roughly on par with a pack of wild dogs).
Second, church is like attending alcoholics' anonymous, only for sin instead of alcohol. Bad people never think they're bad, no matter what they do. Hitler thought he was an awesome guy, and the rest of the members of the National Socialist Party agreed. Nobody knows if Stalin thought poorly of himself, but you can bet he didn't lose any sleep over the millions of people he killed. As you live out your life, it is inevitable that you will, sooner or later, do someone else wrong - and good people are the ones who feel guilt about it. Religion serves to remind bad people what they are, because they do not have their own conscience to remind them.
So why do religious people mistrust atheists? Because, for one, their social structures are strongly rooted in religious activities. Humans instinctively mistrust people who exhibit antisocial tendencies. Secondly, the 'bad' Christians who are only held in check by their weekly sermon simply assume there is no supernatural force keeping that atheist from murdering the people around him, which means he obviously is doing so.
But this intolerance you attribute to "this country" is hardly evident on this forum. If you actually paid attention to threads about religion you'd notice that there has been a major balance shift toward atheism recently, which is why I argue on the opposite side these days. Nobody is intolerant toward atheism here. Even I am not intolerant toward atheism, but what I am intolerant toward is the significant proportion of atheists who are in fact illogical mouth-breathing knuckle-dragging morons who think they're more enlightened than their bible-thumping brethren while neither of them have even a passing comprehension of their own religion or any other.