Jefferson was accused of not being a Christian during the election of 1800. The irony is that his opponent, John Adams, was less of one (in terms of Trinitarian orthodoxy). Allegations against Jefferson were so prominent during that ugly campaign that the gist of them is still remembered to this day: that Jefferson was allegedly an infidel. This is a false but stubborn legacy.
Jefferson biographer Merrill Peterson comments: “For nearly a decade the Federalists had been fashioning an ugly image of Jefferson. Little was added in 1800, but everything was raised to the nth dimension. The fear and distrust dedicated Federalists felt for Jefferson presumably had psychological validity in the Federalist political mind.”
In his book, Separation of Church and State, Phillip Hamburger states: “Many Federalist clergymen claimed that Jefferson was not a Christian, and they thereby introduced into a national political campaign the old issue of religion’s civil importance.”
 The only real reason Adams has not been lumped with Jefferson among Founding Father skeptics is because a majority of northerners supported his party, and southern Republicans did not respond with similar smears.
 Merrill D. Peterson, Thomas Jefferson and the New Nation: A Biography (New York: Oxford University Press, 1970), 636-637.
 Phillip Hamburger, Separation of Church and State (Cambridge, MA: Harvard University Press, 2002 / 2004), 112-113.