This was the beginning of Jefferson unjustly (in part) gaining a reputation as a skeptic.
Daniel Dreisbach is a professor of justice, law, and society at American University and author of Thomas Jefferson and the Wall of Separation of Church and State. He wrote a lengthy article for Christian History & Biography Magazine on the 1800 election and the religious controversy: “In few, if any, presidential contests has religion played a more divisive and decisive role than in the election of 1800. Jefferson’s religion, or alleged lack thereof, emerged as a critical issue in the campaign.”
For example, Dreisbach points out: “In the days before the election, the Gazette of the United States, a leading [Philadelphia-based] Federalist newspaper, posed the ‘grand question’ of whether Americans should vote for ‘GOD—AND A RELIGIOUS PRESIDENT [John Adams]; or impiously declare for JEFFERSON—AND NO GOD!!!’” Even as early as 1798, the president of Yale, the normally wise Rev. Timothy Dwight feared that if Jefferson became president, “we may see the Bible cast into a bonfire, the vessels of the sacramental supper borne by an ass in public procession, and our children . . . chanting mockeries against God . . . [to] the ruin of their religion, and the loss of their souls.” It must be noted that Dwight did not give specific criticism of Jefferson’s religion, but he more broadly expressed worry over what he perceived as a party of leaders emerging who seemed too silent regarding the anti-Christian behavior of the French Revolution, and other cultural trends that seemed to threaten the Christian status-quo of America. It is true that Jefferson did not disavow the French but neither did he affirm their excesses. And it must be noted that Dwight’s predecessor at Yale, Rev. Stiles, held a view of the French more like Jefferson, and indeed supported Jefferson for President.
REV. LINN AND REV. MASON
Although many of the ministers accusing Jefferson of unbelief hailed from New England, two of the most prominent names were ministers from New York. Hamburger notes, “The onslaught against Jefferson began in earnest when Federalist pamphlets charged that Jefferson was a deist and an infidel. William Linn and John Mitchell Mason—the one a Dutch Reformed pastor in New York City, the other a Presbyterian minister of the city’s Associate Reformed Church—initiated the assault, and numerous other Federalists quickly joined the fray.” The attack by Rev. William Linn was the most unexpected in light of previous friendly correspondence and cooperation with Jefferson. The content of Linn’s earlier letters offer no explanation or hint of any discomfort with Jefferson’s faith.
But in the 1800 election season Linn warned: 
- “the election of any man avowing the principles of Mr. Jefferson” would “destroy religion, introduce immorality, and loosen all the bonds of society.”
- a vote for Jefferson “must be construed into no less than rebellion against God.” He feared the “destruction of all social order and happiness.”
Second, there were similar dire predictions from Rev. John Mitchell Mason:“By giving your support to Mr. Jefferson, you are about to strip infidelity of its ignominy. . . . By this act, you will proclaim to the whole world . . . that you do not believe it subversive of moral obligation and social purity.”
Rev. Mason saw a Jefferson victory as “a crime never to be forgiven,” that the people would transfer the presidency “upon an open enemy to their religion, their Redeemer, and their hope, [and it] would be mischief to themselves and sin against God.” The Virginian’s “favorite wish,” according to Rev. Mason, is “to see a government administered without any religious principle among either rulers or ruled.” He charged (partially correctly) that Jefferson’s perspective is: “Religion has nothing to do with politics.”
 Daniel Dreisbach, “The Wall of Separation,” Christian History & Biography Magazine, Issue #99, 2008. https://www.christianhistoryinstitute.org/uploaded/50b787762dbd67.76222839.pdf
 Hamburger, Separation of Church and State, 113.
 William Linn, Serious Considerations on the Election of a President: Addressed to the Citizens of the United States (New York: 1800), 24.
 John Mitchell Mason, The Voice of Warning, to Christians, on the Ensuing Election of a President of the United States (New York: 1800), 35.