It was traditional shortly before the Revolution and in the early Republic because of the French and Indian Wars (what Churchill called "The First World War"). You can see the graves in colonial cemeteries.
By the Civil war the animus had ended in large parts of New England. When Catholics built St. Mary's on Hillhouse Avenue in New Haven--the best area of the city and a short walk from Grove St cemetery where 17th c divines were buried--the local paper defended Catholics from charges in the New York Times that Catholics were being uppity.
The whole Catholic school system was started because of anti Catholic discrimination in the public schools.
It was always a tradition.
MD was founded as a “Catholic” colony (i.e., by Catholics with toleration - hence “the Free State”) in 1632, but by 1700 the Catholics who granted non-Catholics “tolerance” had been dislodged from any power positions and laws emplaced to keep them out. This didn’t change until the RevWar, essentially.