" "In every country and in every age, the priest has been hostile to liberty. He is always in alliance with the despot, abetting his abuses in return for protection to his own. It is error alone that needs the support of government. Truth can stand by itself."Thomas Jefferson - in a letter to Horatio Spofford, 1814 "
I take it that Jefferson was not speaking there about all Christian ministers, but instead chiefly the Catholic ones who entitled themselves "priests", though in this inclusive to large extent of Anglican Catholics in addition to Romanist Catholic priests yet more acutely (for the latter).
The key operative phrasing in his expressed thinking being; "...in alliance with the despot, abetting his abuses in return for protection to his own."
Otherwise; the free exercise of religion, in the same 1st Amendment which protects the freedom of speech, is likewise, similarly protected.
https://www.law.cornell.edu/constitution/first_amendment
Jefferson had no opposition to the Bill of Rights, but rather had encouraged Madison (Madison, who it is generally understood is the author of the first proposed form of the Bill of Rights);
http://civilliberty.about.com/od/firstamendment/f/first_amendment.htm
The idea was, in my understanding, that Jefferson was not impressed upon by priests who hid behind the bible when it suited them, or used the bible to get their way.
Catholic or not, it was the idea of the clergy using the Bible as a way to protect themselves (or the despot) from the law, or scrutiny. Truth can stand by itself, it does not need a bible or scripture or a priest in any case to intervene on it’s behalf.