I think the point may be that systems which produce such behavior are perversions, rather than expressions, of whatever essential nature humanity may be said to have.
> Bregman's digging into subsequent critiques of the [Milgram] experiment revealed that it was not quite as bad as it seemed: a substantial proportion of the "torturers" had figured out that it was not real. Several more protested that it was wrong. Those who did continue were convinced by the researchers that what they were doing was for the greater good. Bregman, with something of a leap, goes from there to the Holocaust and the trial of Adolf Eichmann in Jerusalem. Bregman is horrified by the Holocaust, as anyone who believes in the goodness of humankind must be. He suggests that people will indeed do nasty things on a mass scale if they are convinced that it is for the greater good. It was not inherent nastiness that led to the Holocaust, Bregman suggests, but years of indoctrination.
Himmler complained obliquely in one of his Posen speeches, I believe, about how difficult this indoctrination was to enforce and maintain. While that's not a source I would ordinarily be happy to cite, this complaint in particular seems not without relevance here.
My guess? Because we've only been at this whole "civilization" thing for a few thousand years, and although that sounds like a hell of a long time when compared with the few dozen years any one of us gets, it has so far not been enough for us to work out how we can reliably generalize at large scale the same altruistic instinct that so often and so regularly leads so many of us to risk harm to ourselves in defense of people we don't even know.
It's probably not a very good guess. But what the hell, at least it's a guess that leaves room for the hope of a better future, and I like that a lot more than any of the alternatives that seem to be at hand.
These systems are produced by people who believe in claptrap like this, that human beings are innately good but merely corrupted by institutions. How many million have died, from "Kulak" farmers to Chinese peasants, as a result of this kind of thinking which blinds us to thinking we can do no wrong?