Because of their unorthodox religious views and their insistence that religious confession was a private matter. Rob Boston has a round-up:
George Washington The father of our country was nominally an Anglican but seemed more at home with Deism. The language of the Deists sounds odd to today’s ears because it’s a theological system of thought that has fallen out of favor. Deists believed in God but didn’t necessarily see him as active in human affairs. The god of the Deists was a god of first cause. He set things in motion and then stepped back.
The Jefferson Bible, aka The Life and Morals of Jesus of Nazareth
John Adams The man who followed Washington in office was a Unitarian, although he was raised a Congregationalist and never officially left that church. Adams rejected belief in the Trinity and the divinity of Jesus ... In his personal writings, Adams makes it clear that he considered some Christian dogma to be incomprehensible. ... As president, Adams signed the famous Treaty of Tripoli, which boldly stated, “[T]he government of the United States of America is not in any sense founded on the Christian Religion”
Thomas Jefferson Our third president did not believe in the Trinity, the virgin birth, the divinity of Jesus, the resurrection, original sin and other core Christian doctrines. He was hostile to many conservative Christian clerics, whom he believed had perverted the teachings of that faith. ... Although not an orthodox Christian, Jefferson admired Jesus as a moral teacher. In one of his most unusual acts, Jefferson edited the New Testament, cutting away the stories of miracles and divinity and leaving behind a very human Jesus, whose teachings Jefferson found “sublime.”
James Madison Unlike many of today’s politicians, who eagerly wear religion on their sleeves and brag about the ways their faith will guide their policy decisions, Madison was notoriously reluctant to talk publicly about his religious beliefs ... Madison was perhaps the strictest church-state separationist among the founders ... He opposed government-paid chaplains in Congress and in the military. As president, Madison rejected a proposed census because it involved counting people by profession. For the government to count the clergy, Madison said, would violate the First Amendment.
