In his magisterial Separation of Church and State (2002), Philip Hamburger demonstrates that anti-Catholic animus contributed significantly to the post-Civil War movement to separate church and state. In the 19th century, this separation was usually between states and “sectarian” Catholic institutions and programs. “Non-sectarian” Protestant institutions and programs were largely exempt.
At the national level, the most notable manifestation of this anti-Catholic animus was the constitutional amendment proposed by Representative James Blaine (R-Maine) to prevent, among other things, public funding of schools “under the control of any religious sect.” Proposed in 1875, the amendment passed overwhelmingly in the House but did not receive the necessary two-thirds majority in the Senate. However, many states soon amended their constitutions to include similar amendments. Missouri did so in the same year that Blaine’s Amendment failed in the Senate.