Here is the issue in a nutshell:
Baptists believe in the separation of church and state, primarily so those wielding government power will not dictate what people can publicly believe. No "You have to be a white male Christian to vote." The constitution says the government cannot establish a required form of belief, such as we all must be Calvinists, nor can the government hinder our free practice of Calvinism or whatever.
So the question is how do publicly funded schools, which means government funded schools, avoid teachings that infringe upon my belief system?
Say I believe God created life. But the public school teaches (indoctrinates?) students that life arose from happenstance
So the only constitutional way of government funding of schools, is to provide the money to the parents, and let them pick the school of their choice, such as a Christian school, or one teaching atheism.