In 1801, Jefferson would become the first executive of the United States to go to war with an Islamic nation. He would also be the first American holder of high office whose political opponents defamed him with accusations of being a Muslim. This experience notwithstanding, he would be the first president to entertain a Muslim ambassador in the nation’s new capital, and in correspondence with Muslim rulers of North Africa he would repeatedly invoke a shared belief in one God. In the conduct of foreign relations, Jefferson had relied on his study of Islam, and when after leaving office he returned to his library at Monticello, he would choose a telling final place in his collection for the Qur’an that had informed his understanding of the Muslim faith.
. . . unbeknownst to Jefferson, by the eighteenth century, Muslims had been analyzing the Qur’an with the aid of a number of other sources for more than a millennium. But such historical particulars would have mattered less to Jefferson than the intellectual imperative to question all faiths, including Islam. What he objected to among Muslims he also faulted among both Jews and Christians: the dangers of a literal adherence to a revealed truth.
. . . In 1802, Jefferson was reminded by his ally the Baptist leader John Leland and his followers of the very real religious intolerance and political inequality they and all other non-Congregational Protestants continued to suffer in New England. . . . Jefferson had reason to fear that the bigotry he had fought his whole life to extirpate might never disappear from the nation. For if Protestants still faced intolerance from other Protestants, what hope for non-Protestants in America.
. . . The liberty I contend for is more than toleration. The very idea of toleration is despicable; it supposes that some have a pre-eminence above the rest, to grand indulgence; whereas, all should be equally free, Jews, Turks, Pagans and Christians. Test oaths and established creeds, should be avoided as the worst of evils. – John Leland, “Virginia Chronicle”: 1790
– Thomas Jefferson’s Qur’an Islam and the Founders by Denise A. Spellberg