Spec. Jeremy Hall, a soldier in Iraq, was prevented from gathering with other atheists and non-Christians, and is basing his lawsuit on practices that discriminate against non-Christians in the military. His First Amendment rights were also frequently violated due to discrimination he faced when refusing to join prayer.
Atheist Revolution reports the full story, as well as Hall's jeopardized safety resulting from his suit against Maj. Freddy Welborn and Secretary of Defense Gates for violating his religious freedom--meaning freedom to both participate in and refrain from religion.
I don't know why it is so difficult to tolerate atheisism. If anything, a group of people who value reason are an asset to society--even if a theist disagrees with one belief in a larger framework that values critical thinking.