“those who live by mystery & charlatanerie, fearing you would render them useless by simplifying the Christian philosophy, the most sublime & benevolent, but most perverted system that ever shone on man, endeavored to crush your well earnt, & well deserved fame”
That was a direct attack on the Church. Jefferson was a Deist who denied the divinity of Jesus. He admired Jesus as a moral teacher, as a mere mortal man. He admired the ‘philosophy’ of Jesus, but viewed Christianity(as a religion) as being the most perverted system ever created.
He wrote his own ‘Jefferson Bible’ that completely excluded any hint of divinity or any miracles. He viewed Jesus merely as a mortal, moral philosopher. He viewed Christianity as being a perversion of the truth (the truth being that Jesus was merely mortal) and a system designed to crush human endeavour.
The Constitution was not drawn up by Christian men and based on Christian values, it was drawn up by Deists, Unitarians and Freemasons. It tolerated the right of people to be Christians (as it tolerated the right of people to be followers of other religions). The Constitution was based on the values of the Enlightenment, not the values of Christianity. The values of the Enlightenment are secular values, their basis runs contrary to the values of the Church.