The "separation of church and state" is not part of the United States Constitution or Amendments.  Rather, this phrase was used by Thomas Jefferson when he wrote to certain Baptists:

Believing with you that religion is a matter which lies solely between Man & his God, that he owes account to none other for his faith or his worship, that the legitimate powers of government reach actions only, & not opinions, I contemplate with sovereign reverence that act of the whole American people which declared that their legislature should "make no law respecting an establishment of religion, or prohibiting the free exercise thereof," thus building a wall of separation between Church & State.2

Far from the present uses of this phrase by atheists, who insist that "separation of church and state" means that there must be no public exercise of religion, Jefferson's use guaranteed the free exercise of religion.  The actual first amendment also protects religion from Government.  The Government cannot establish religion, or prohibit the free exercise thereof.

Isn't it amazing how people can twist things?