Take for example the Ford religion seen in Huxley's Brave New World, where the economic and political ideas of Henry Ford are taken to the level of religious doctrine, and anyone deviating from the established way of life, and the accepted social principles, they are faced with a sort of inquisition that ends in exile and ostracism. Another very clear example is the entire society portrayed in, once again, Margaret Atwood's The Handmaiden's Tale, with an enforcement of some of the most conservative, orthodox and restrictive ideas of American religious history, from total oppression of women, mandatory daily group prayers, among other such endeavors.
The results from these religious societies turn out to be some of the most oppressive, restrictive, and controlling societies out there. This is probably the sum of all other fears Sci-Fi has, and the worst of it is that given the religious background of it the passions involved in that society can be raised to the point of fanaticism, and no matter what reasonable explanations are given for behaviors other than those approved by society they can only be condemned and persecuted.
Have you come across any other stories where religious zealotry is a central element of the story? What else could be covered by zealotry and fanaticism? Is there space for this kind of social behavior only in Dystopia?