I don't think the kind of thinking you describe is limited to religion. While it might be reinforced or encouraged by many religions, it is also reinforced and encouraged in many places in our culture. From a young age, children are taught to obey adults more or less without question and taught to respect and trust authority figures such as police, teachers and government officials. Most people, at least in our country, are not taught critical thinking from a young age and are taught not to question things.

When I went into the military, I had a lot more problems than most of the recruits with the authority aspects, but I kind of expected that going in and forced myself to adapt to it. When I got out, I was shocked when I went to college and found the mentality wasn't all that different. I had always had the impression that college was supposed to be a place where ideas and debate were welcomed and creativity encouraged. As it turns out, most college students have no ideas or creativity, they show up to class and simply accept what the professor says without question and follow the steps they learned in high school to get high GPAs regardless of whether they are learning anything.

It is also why I have a terrible record at being employed by other people. I never fit in well with the "do what the boss says" and time clock mentality that pervades corporate America. Even as an employer, I find it really difficult to find employees that don't require hand holding and want a supervisor to okay every little decision they make. I don't know if such attitudes are nature or nurture, but it drives me absolutely nuts and it certainly seems to be prevalent both in religion and outside of it. 

i'm only just now, at the age of 31, beginning to suspect i might be an intellectual, in that i'm beginning to develop my own ideas and worldview in a systematic, communicable way.  one literal meaning of "intellectual" is having a developed faculty for discrimination, which requires dispassionate objectivity.  one must learn to take each situation, each individual, each continuum as a thing-in-itself, and only apply syllogisms when direct perception is either impossible or exhausted.

if x self-identifies as a christian, muslim, jew, democrat, republican, physicalist, spiritualist, or what have you, these labels might be useful in an auxilliary way, but the fact that x is x trumps everything else.  is x pleasant?  is x reliable?  is x honest?  is x useful?  is x altruistic?  is x nonviolent?  is x compassionate?  if so, then in my position as a humanist, i can find no fault with x.  i'm essentially a conservative person (i don't mean that politically), and one thing my studies of buddhism have convinced me of is that a thing is inseparable from its constituent parts.  therefore, if x fulfills my above humanistic criteria of what constitutes "good," then changing x, making x an atheist rather than a christian, for example, or a democrat rather than a republican, might just as easily do as much harm as good.  in other words, if it ain't broke, don't fix it.

an example of a common syllogism found in many people's thinking on this site is,

christianity is at root harmful;

x is a christian;

therefore, were x not a christian, he would be less likely to do harm.

such syllogisms cannot stand up to direct perception of x in terms of calculating his capacity for doing good.  if i perceive x never does harm, that invalidates the inference that x must be ultimately harmful, or have more capacity to harm, because he is a christian.  indeed, it makes the syllogism useless. 

how can we move from inferential knowledge to superior perceptual knowledge?  get to know x.  there's no other way.