I think that this is an application of the changing circumstances argument to culture. For most of human history the challenges faced by cultures were along the lines of "How can we keep 90% of the population working hard at agriculture?" "How can we have a military ready to mobilize against threats?" "How can we maintain cultural unity with no printing press or mass media?" and "How can we prevent criminality within our culture?"

Individual rationality does not necessarily solve these problems in a pre-industrial society better than blind duty, conformity and superstitious dread. It's been less than 200 years since these problems stopped being the most pressing concerns, so it's not surprising that our culture hasn't evolved to create rational individuals.