Jefferson did more than refer to it in some letters. He stated it in letters and speeches when he was President. Additionally, James Madison referred to "the total separation of the church from the state." When he was President in 1822, he said, "...religion & Gov will both exist in greater purity, the less they are mixed together."
And in Reynolds v US, the Supreme Court has referred to Jefferson's phrase as the true meaning of the First Amendment.
As for those symbols, we were a country founded by Christians, so they used Christian phrases. However, God wasn't added to the Presidential oath until the mid 1800s and He wasn't in the original Pledge of Allegiance either.
As Jefferson said, religion is a matter which lies solely between man and his God. In other words, private, personal.
Except the secular left overplays that. For example, they argue that since those who are against gay marriage or abortion are so usually because of religious belief, their stance on these issues should be dismissed altogether. That's what I mean when I say they try to isolate religion. There's a difference between the government establishing a religion (like a state religion) and religious beliefs having influence. In the south, you'll have a strong Baptist influence. In Boston, a strong Catholic influence. In Utah, a strong Mormon influence. None of this is automatically unconstitutional.
