Nothing says those who do not want pray have to pray. By the same token, nothing says President Bush can't ask people to pray. Mr. Bush didn't give up his right to free speech when he got elected.
You can ask me to give you a million dollars and I can say no. President Bush can ask people to stand on their heads. People are free to do it or not.
The constitution bars the president from ordering anyone to pray. It does not bar him from asking, any more than it bars me or you from asking.