In my reading, Crichton was complaining about rigid and intolerant people who claim special access to "the truth" - access which they feel is self-evident and not subject to criticism.
Crichton, as is the case with much of the secular world, characterizes this mind-set as religious - wrongly. There are many, many believers who are open-minded and tolerant and many athiests who are not. But he is not without justification. For centuries religious believers held power - and too often abused that power to suppress and persecute dissident voices.