Notice the word "especially". Scientology is based on the idea of what some might call aliens having superhuman powers. In atheism, a number of superhuman powers, i.e. things that humans cannot do, are ascribed to science- even though there is nothing that disallows that God could be involved in everything from the big bang to evolution, somehow the Big Bang and Evolution take on a life of their own, without full understanding of them.
Darwin takes the place of a prophet, although Darwin himself was not an atheist [1] and said, "Science has nothing to do with Christ, except insofar as the habit of scientific research makes a man cautious in admitting evidence."
Faith and science can co-exist, but atheism has a belief that they can't. They put up billboards, organize, take donations, have musical rallies at military bases with atheist songs, and pass out literature like evangelical religions. And they are as intolerant and unaccepting as well. I find them quite obnoxious, but atheism is a religion, therefore according to our freedom of religion, it must be allowed, but it should be allowed along with the free practice of any other religion in any place, at any time, in any public place.
[1] http://en.wikipedia.org/wiki/Religious_views_of_Charles_Darw...