The extreme hostility towards atheists in America can be traced in part to two related factors: America's view of itself as a religious nation entrusted with a special mission from God and America's fight against communism in the Cold War. These two combined to portray atheists as a godless enemy, a fifth column either for Satan or for totalitarian communism. This remains true even today when there is no "commie menace" pointing nuclear weapons at America. A good enemy is hard to give up.
During the earliest years of the Cold War there were few overtly religious arguments against communism. Not until the early 1950s did religious and political leaders realized how religious opposition to communism might become a stronger than political opposition. Arguing that communists as evil because of being godless, though, required transforming anti-communism into anti-godlessness and this meant turning America even more against atheists, agnostics, liberal believers, and skeptics of various sorts. Religious doubters were transformed into not just an enemy of religious institutions, but of political institutions as well.
It's curious that Christians would insist that their religion be connected to capitalism. No longer are faith in Jesus and God sufficient to be a "good Christian"; now, one must also have faith in market capitalism and small government. Since so many of these Christians assume that anyone who disagrees with them on any one point must disagree with them in everything, it isn't surprising that some assume that an atheist or humanist must be a communist. This isn't helped by the fact that 20th century communist governments been almost entirely atheistic in nature
This Cold War legacy continues to affect atheists in America today. It's not hard to still find Christians attacking atheism as essentially socialist or communist in nature, arguing that atheism should be rejected because socialism and communism are evil. One would almost think that the Cold War hadn't ended with an American victory and collapse of the Soviet Union. Now, though, anti-atheist bigots also have a need to associate atheists with whatever threat they see as the most serious one facing them. Instead of tarring atheists with the "commie" label, it's getting more common to see Christians claim that atheists are in league with Muslim extremists attacking the West. Muslims hiding under the bed doesn't make for as enduring an image as commies hiding under the bed, though.