Public schools at the time taught a generic form of protestantism. It was not considered an establishment of religion because no specific denomination was being taught or adhered to.
This subsequently changed when agnostic or atheistic forces worked for a complete separation of schools from any form of religion. There is a book by a fellow named Hamburger titled “Separation of Church and State” which goes into the history of the change from individual state established religion to our present situation. Many states, like Connecticut, Virginia, etc. at one point had established churches. The constitution was only applicable to establishment by the U.S. goverment.
