The question is whether open or implied atheist advocacy in public school can violate the establishment clause. The whole basis for the Dover decision was the idea that ID content has to be kept out of the public school classroom because those who supported it were motivated by a desire to promote religious belief. In a court case it was successfully argued that you atheism is protected by the free exercise clause, in a case where an atheist prisoner was granted access to atheist materials.
Now, in the Constitution, the free exercise clause and the establishment clause go together. Heck, they're in the same sentence. Atheists can't help themselves to the free exercise clause, but when accused of violating the Establishment Clause on behalf of atheism, fall back on the "not collecting stamps" argument. That's cheating.
So, as I keep saying, the main argument in the Dover case, which was an Establishment Clause case, only works if you assume the religious neutrality of evolutionary biology. That is the official NCSE position on the compatibility of religion and evolutionary biology that people like Dawkins, Myers, and Coyne are hell-bent on attacking.
Given the constitutional context here, the fact that atheism is not a religion in the popular sense is irrelevant. If you want Free Exercise protections, you have to live with Establishment Clause limitations. It's the American way.