Public schools provide students with a conceptual net constructed almost entirely from scientific method. And when we teach students to think in entirely secular, scientific ways about history, nature, psychology, morality, and society, it should come as no surprise that after 12 years they conclude that there are no religious fish to found in the sea. Or if there are, one must accept their presence as a matter of faith. Consider miracles, for example. While we might put nature on the rack to make her divulge her secrets, as Francis Bacon once recommended, we cannot force God to replicate miracles.
Miracles fit into a different pattern of intelligibility than that provided by modern science.
Indeed, what may be irrational to believe given scientific method and universal laws of nature might be rational to believe from within a religious world view given the unfolding story and the religious power of the experience. Public education does not indoctrinate students by attacking religion or promoting a militant secularism. It fails to provide students with the intellectual and emotional resources that would enable them to take religion seriously. It is not enough to teach students something of the role of religion in history. Students must learn something about contemporary religious ways of thinking about virtually all aspects of life.