There have been some very interesting developments counter to this in recent years, and I hope that they gain some traction. There's a program in the UK called Cognitive Acceleration [1] that seems to have a lot of promise for developing more of a habit of independent thinking. There's also some interesting stuff coming out of Harvard called Visible Thinking [2] that I believe is very beneficial.
Unfortunately, I think it will be quite a while before that kind of thing is widely adopted because of sheer momentum and the apparent drive toward ever more standardized testing.
I'm sure there are dozens of other factors that contribute to what you're talking about, but schooling is one that I recognized as having a huge impact on my own life in terms of my perception of my position relative to authority.
[1] http://www.teachingexpertise.com/articles/cognitive-accelera...
[2] http://www.old-pz.gse.harvard.edu/vt/VisibleThinking_html_fi...