Challenge a person's beliefs, and you challenge his dignity, standing, and power. And when those beliefs are based on nothing but faith, they are chronically fragile. No one gets upset about the belief that rocks fall down as opposed to up, because all sane people can see it with their own eyes. Not so for the belief that babies are born with original sin or that God exists in three persons or that Ali is the second-most divinely inspired man after Muhammad. When people organize their lives around these beliefs, and then learn of other people who seem to be doing just fine without them--or worse, who credibly rebut them--they are in danger of looking like fools. Since one cannot defend a belief based on faith by persuading skeptics it is true, the faithful are apt to react to unbelief with rage, and may try to eliminate that affront to everything that makes their lives meaningful.
Thinking is computation, I claim, but that does not mean that the computer is a good metaphor for the mind. The mind is a set of modules, but the modules are not encapsulated boxes or circumscribed swatches on the surface of the brain. The organization of our mental modules comes from our genetic program, but that does not mean that there is a gene for every trait or that learning is less important than we used to think. The mind is an adaptation designed by natural selection, but that does not mean that everything we think, feel, and do is biologically adaptive. We evolved from apes, but that does not mean we have the same minds as apes. And the ultimate goal of natural selection is to propagate genes, but that does not mean that the ultimate goal of people is to propagate genes.
Institutionalized torture in Christendom was not just an unthinking habit; it had a moral rationale. If you really believe that failing to accept Jesus as one's savior is a ticket to fiery damnation, then torturing a person until he acknowledges this truth is doing him the biggest favor of his life: better a few hours now than an eternity later.