Many people cite Jefferson for the “wall of separation” doctrine regarding religious matters and its relationship to the state. This interpretation is novel and interesting, but unconvincing. (At the founding the official state church of Massachusetts was Puritanism and that was A-OK). The real development of this doctrine was in the 1940s as a part of sweeping anti-Catholic bias of the KKK (they didn’t just go after blacks, after all).
The phrase found its first use in the opinion of the court written by Klansman Supreme Court Justice Hugo Black in Everson v. the Board of Education. This ruling specifically targeted Catholic schools as he was worried about a coup from Catholics.
I wonder if the ACLU realizes that they generally defend a KKK invented legal doctrine that was used as a part of religious discrimination.