Therefore nothing, it doesn't apply to them. Like the plumbing code doesn't apply to tree surgeons. Religious freedom is the freedom to worship God. It doesn't include the freedom not to worship God - you don't need a 1st Amendment for that. In addition, not doing something is not the same as doing something. So atheism is not the opposite of religion - atheism has nothing to do with religion, and should not be included in any category with it. Rejecting God is not a religion.
Of course, I'm not talking about the free speech part of the 1A, that's universal.
Let me make sure I understand...are you arguing that a law mandating the worship of God would be constitutional?
I believe the decision can work in the favor of Christians since disallowing the teaching of theistic explanations in publicly funded venues can now be said to be establishing atheism as the official religion in those venues.