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.
Why should the spread of ideas and people result in reforms that lower violence? There are several pathways. The most obvious is a debunking of ignorance and superstition. A connected and educated populace, at least in aggregate and over the long run, is bound to be disabused of poisonous beliefs, such as that members of other races and ethnicities are innately avaricious or perfidious; that economic and military misfortunes are caused by the treachery of ethnic minorities; that women don't mind to be raped; that children must be beaten to be socialized; that people choose to be homosexual as part of a morally degenerate lifestyle; that animals are incapable of feeling pain. The recent debunking of beliefs that invite or tolerate violence call to mind Voltaire's quip that those who can make you believe absurdities can make you commit atrocities.
Many textbooks point out that no animal has evolved wheels and cite the fact as an example of how evolution is often incapable of finding the optimal solution to an engineering problem. But it is not a good example at all. Even if nature could have evolved a moose on wheels, it surely would have opted not to. Wheels are good only in a world with roads and rails. They bog down in any terrain that is soft, slippery, steep, or uneven. Legs are better. Wheels have to roll along an unbroken supporting ridge, but legs can be placed on a series of separate footholds, an extreme example being a ladder. Legs can also be placed to minimize lurching and to step over obstacles. Even today, when it seems as if the world has become a parking lot, only about half of the earth's land is accessible to vehicles with wheels or tracks, but most of the earth's land is accessible to vehicles with feet: animals, the vehicles designed by natural selection.
The task of evolutionary psychology is not to weigh in on human nature, a task better left to others. It is to add the satisfying kind of insight that only science can provide: to connect what we know about human nature with the rest of our knowledge of how the world works, and to explain the largest number of facts with the smallest number of assumptions.