The early public school system did not take long to land in religious dispute, and religious accommodation conflicts continue today. Public schools were originally instituted by a Protestant majority and reflected Protestant religious viewpoints, including mandatory daily readings from the King James Bible. In the early 1820s, New York started funding schools, and by 1840, some Catholics were objecting to the Protestant religious curriculum. The Protestant majority protected its turf by denying funding to “sectarian” schools (as though the Protestant public schools were not sectarian), “including Baptist, Methodist and Catholic.” Over the succeeding years, the political will to prevent funding for any schools other than the Protestants’ was distilled into an anti-funding drive aimed mainly at Catholics.

Some Christians in the United States might be tempted to latch onto the early Protestant practices in the schools as proof that the schools should now reintroduce prayer and religion in the schools. They argue that public education has been corrupted, because prayer and Bible reading were held unconstitutional. The now-deceased Rev. Jerry Falwell, following 9/11, remarked: “We have seen the course of secularism in our schools, and it is obviously time for a change. It is high time our nation once again favors its people of faith by allowing our public-school students to be exposed to prayer and the pursuit of faith.” Mississippi Governor Kirk Fordice opined: “‘one day, I hope soon, it's not going to be legal to keep prayer out of public schools.’” The Rev. Louis Farrakhan also has urged a return to prayer in the public schools: “Thomas Jefferson was rooted in the Gospel of Jesus Christ even though he didn't apply it to his slaves.