Ricky Gervais was discussing atheism with someone who's a believer and Gervais said "You don't believe in more than 4000 religions and I don't believe in only one". By not respecting a particular religion, it's not necessarily respecting atheism, it could be respecting any of the others.
Many of the founding fathers were Freemasons, who don't necessarily promote a particular deity, but they do believe in a higher power.
From the link, "Deism was popular at the time – the belief in God as the creator of all things, but not as a miracle worker or one that answers to prayer." and "The Constitution even bars all laws from “respecting an establishment of religion,” while also protecting “the free exercise thereof.”
The text of the U.S. Constitution makes no mention of God, Jesus Christ, or Christianity.
allthatsinteresting.com