Here is a quote from John Ferling's Adams vs. Jefferson, page 153-154:
The Federalists also fixated on Jefferson's religious beliefs, maligning him as an atheist. This was grounded on what Jefferson had written in Notes on the State of Virginia, drafted in 1782 and first published in the United States in 1788. Jefferson had lauded the Virginia Declaration of rights of 1776, which provided for religious toleration, but, wishing to go further---he hoped for a law that would separate church and state---Jefferson had dilated on the "rights of conscience," about which individuals were "answerable [only] to...our God" and never to the state. He then added that "it does me no injury for my neighbor to say there are twenty gods, or no God. It neither picks my pocket or breaks my leg." These two sentences were reprinted endlessly in Federalist newspapers as proof of Jefferson's impiety. In addition, Federalist scribes cautioned that Jefferson viewed the clergy as "curses in a country." Primarily, however, they depicted him as a "howling atheist" and "infidel." Filled with contempt for Christ, Jefferson supposedly embodied iniquities that would bring on the moral decline of the United States. In New England people were told to hide their Bibles should Jefferson be elected, and the warning went out that his election would call down God's vengeance on the United States.Though more from the pulpit than the press, lurid tales were told of bizarre worship services at Monticello at which Jefferson supposedly prayed to the Goddess of Reason and offered up dogs on a sacrificial altar. One Federalist newspaper advised its readers to vote for "GOD---AND A RELIGIOUS PRESIDENT or impiously declare for JEFFERSON--AND NO GOD."
How many current cultural tropes did you notice there?
Thomas Jefferson, never self-identified as an atheist, as far as I know. The conflation of religious tolerance and freedom with repression felt by the dominant religion was as real then as it is now. We are not dealing with anything new, in talking about this religious privilege and the association with separation of church and state with impiety and even lack of patriotism.
There are simply some people, whether in 1800 or 2013, who simply cannot see that asking for religious neutrality from our government is a good idea. Those that declare the United States to be a Christian nation have the precedence of idiots from the 18th century who did not grasp the importance of said separation then, and who wanted a Christian president rather than a supposedly godless president. And those who see the legal foundations of the United States as secular, as its founding documents state, have the precedence of people like Jefferson and Madison on their side. It's not simply that we were a secular nation and people forgot, it's that some people simply could not grasp it at the time, and that tradition seems to have run parallel to the actual law and history.
In short, there are always idiots in society, and it may be the case that they will never go away. One of the weaknesses of democracy is that those idiots also get to vote, and thus we have Michel Bachmann and Rick Perry.