I believe there is a meaningful difference between, on the one hand, teaching children the scientific method - how to explore and try new things, and abandon them if they don't work - how to seek one's own inner truth, and how to be tolerant of others' difference in habits and cultures, vs. on the other hand, teaching children that the infallible word of God was written down 2000 years ago, and never amended since, and that the slightest deviation from it will result in eternal hellfire - not only for those who outright reject the message, but even for those around the world who live out their entire lives having never been exposed to it.
One path leads to continued progress for humanity. The other path leads to stagnation and an endless repetition of the sorriest chapters in human history: only now, with nuclear weapons involved, and in the hands of several different nations, the annihilation of humanity is a distinct possibility.
You can't both-sides it. They're not the same.
However, from the perspective of a religiously-indoctrinated person, science and liberal principles of tolerance and anti-bigotry would naturally appear to simply be the flip side of the same coin of indoctrination. Having never been taught otherwise, such people have no reference for processing information outside of a propagandistic framework.