Therefore...what, exactly?
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.