On Institutional Loyalty and Bias

Short post today - just a personal gripe.  One of the most common "popular" arguments against religion in general is to complain that no "free thinking" person would believe in it.  The insinuation is that people of a religious bent are not free thinking, but are "indoctrinated" by institutions that "control" what they are allowed to say or believe.

In contrast, the "free thinker" is liberated from these institutional controls to pursue truth wherever reason or science or whatever truth-mechanism they follow would lead them.

This shows up in television (shows as different as House or Battlestar Galactica), and in real debates (it was forwarded as an argument against a Jesuit professor by an atheist scientist on "60 Minutes" just a few months ago).  The implication is that institutional bias compromises religious thinkers and therefore makes their beliefs (including their religious ones) untenable, at best, if not laughable.