Teaching critical thinking in school can't stand up to the power of indoctrination by Mom, Dad, and God at home. Religious parents actively work to ensure that their children see them (and the church) as the only authoritative source of truth. They may learn to question "authority", but not "Authority".
With Devos using the public school system to further the kingdom of God and maximize "Kingdom Gain" in this country, even the rational teacher will be powerless to stop the next generation of dogmatic, mindless drones from growing and running the country.
Religion, the simultaneously mocked and mildly feared boogeyman of Slashdot. Kids go their own ways. Most go through a rebellious phase in their teens where they reject their parents point of view and explore other views. Most things have an agenda, both public and private schools. Some parents have a religious agenda while others, who share your world view, have a religious phobia. Some are right leaning, others left leaning. Life still goes on and society hasn't died. For what it's worth I've found churches to be among the best examples of bringing different groups of people together in relative harmony.