From the Witherspoon Institute:
Notwithstanding his unorthodox views of Christianity, Thomas Jefferson staunchly adhered to the rights of all religious believers, Christian and non-Christian alike, to free religious exercise.
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[I]t is imperative to distinguish the long-simmering contention and disagreement over Jefferson’s beliefs on religion from his clear public support for religious liberty. When it came to religious freedom and rights of conscience, Jefferson was both a strong critic of official government establishments of religion and a staunch proponent of the free exercise of religion.
When the Constitution was drafted in the summer of 1787, Jefferson was in Paris serving as ambassador to France. Two hundred twenty-five years ago this month, he wrote James Madison to share his thoughts on the recently proposed Constitution. Jefferson’s first and most central complaint was “the omission of a bill of rights providing clearly … for freedom of religion” and for other rights and liberties.