It restricts the powers of Congress. It does not restrict the powers of individuals, or of religious bodies, except for eliminiating the possibility of using Congress as a tool of religious persecution.
That said, I am a Christian, and I want the words out, too, because they insult God, by intentionally[2] implying that some nations might not be "His" care and authority (a notion contrary to Sacred Scripture)!
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HadEnuf
[1] Or "the", according to some sources contemporary to the ratification.
[2] It's ugly, but it's true: it was a way to slap the "godless commies".