Which book are you talking about?It's a good book, an excercise in rationality, if you like that sort of thing, and it's very readable and entertaining. I don't need to tell you that the brainwashed argument doesn't hold up, one is free to read any book they like and not be tied to one text and outlook. Also the scientific method relies on verifiable evidence that's always incorporating new knowledge, it isn't fixed and rigid, so its hardly brainwashing. If there was evidence for a God, it would quickly be incorporated into scientific teaching.
I definitely agree about the scientific method and I find it ridiculous when it is dismissed by religious fanatics. I’ve even seen supporters of Young Earth Creationism accuse those who understand evolution as having a religion, even calling them “evolutionists.” It undermines their own position to call evolution a religion.