There is no constitutional protection for atheism. Asserting that tax exempt status for religious organizations equates to government sponsorship of a particular religion is simply false. Neither does it support the assertion that the Government is advocating belief in religion over atheism. More than a few atheistic not-profits also benefit from the same law.
Constitutional protection for atheism falls under free speech. Atheism is simply the absence of belief based on lack of evidence. It's not a belief in anything. It's a non-belief. Not the same thing as religion. For example, of the approximate ~1400 recognized deities, Christians are 'atheistic' of 1399.