And there are many other founding father who had no problem mixing church with state:
http://www.wallbuilders.com/LIBissuesArticles.asp?id=8755
there is an argument that can always be made from both sides.
The vast majority of those quotes are concerning their own religious beliefs. "I have examined all religions, and the result is that the Bible is the best book in the world." "I . . . [rely] upon the merits of Jesus Christ for a pardon of all my sins." "I am a Christian in the only sense in which He wished anyone to be: sincerely attached to His doctrines in preference to all others."
There is no doubt that the majority of the founders were Christian (although many of those founders who were quoted, such as Washington, Franklin, and Jefferson, were actually deists or had a very distinct religious belief that was loosely based on Christianity). However, history does not reflect that their desire was to incorporate Christianity or any specific religion into our government in any way. Regardless of their personal beliefs, they made it clear that those should remain as personal beliefs, and not be espoused or favored by the government.
Afterall, that site full of quotes includes religious statements from Jefferson, who actually originated the "separation of church and state" phrase. Or Madison, who said that the government functions with complete success "by the total separation of the Church from the State." Or Franklin, who posited that a religion should be able to support itself, and that if it can not support itself, then it is not a good one. We can paint the founders as Christians all day, but it doesn't affect their political stance regarding the separation of church and state.