Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof...
The first phrase forbids Congress from creating a national church along the lines of the Church of England. The second phrase guarantees the free exercise of religion.
There is nothing here that would stop Congress from banning or severely limiting the free exercise of atheism. The idea that freedom of religion implies freedom from religion is a comforting fiction.
You could, and I imagine many of you will, argue that atheism is covered by the next phrase in the amendment concerning freedom of speech and of the press and therein lies the Constitutional protection of atheism. But that does not actually address atheism whereas the opening phrases are specific to religion. This places religion in a separate category from free speech. A category in which atheism is not included.
Instead, the phrase refering to protecting the 'free exercise of religion' could well be interpreted as prohibiting atheism and/or the free discussion of atheism with religious people.