The initial movement to keep prayer out of public schools
Political positions change over time. For example, some people who condemn the Republican party as racist and praise the Democratic party for its inclusiveness are surprised to learn about the origins of the Republican Party. While it would be a stretch to claim that the initial Republicans promoted equality of the races, and while there was self-interest involved, the fact remains that one party was more favorably inclined to the emancipated blacks during Reconstruction than the other.
Then there is the long-standing debate on the proper role of religion in American society, and what the religious clauses to the First Amendment actually mean. This debate has resulted in statements such as this:
The public school system of the several states is the bulwark of the American republic; and, with a view to its security and permanence, we recommend an amendment to the constitution of the United States, forbidding the application of any public funds or property for the benefit of any school or institution under sectarian control.
And no, this wasn’t the position of some obscure kooks – this was in the party platform of a major party.
Specifically, the Republican Party, in its 1876 platform.
However, the party had changed its tune by 1892:
The ultimate reliance of free popular government is the intelligence of the people, and the maintenance of freedom among men. We therefore declare anew our devotion to liberty of thought and conscience, of speech and press, and approve all agencies and instrumentalities which contribute to the education of the children of the land, but while insisting upon the fullest measure of religious liberty, we are opposed to any union of Church and State.
As you can see, by 1892 the Republican Party was not only opposed to religious influence upon public education, but was also opposed to religious influence upon any governmental entity.
See Warren Throckmorton’s blog post for more details.