Actually, Jefferson also used the word "God" in the preamble to the Dec of Ind. Not that it matters.

Text of the 1st Amendment:
"Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof;..."

It seems like forbidding prayer in schools or otherwise restricting religous practices through an act of Congress, could be construed as "prohibiting the free exercise thereof." Just how you look at it I guess.