The original poster here seemed to basically be saying "This is a minor effect of such complexity that it could be entirely the result of selective pressures on other parts of human psychology, which give us this predisposition." This seems highly plausible, given that I don't think anyone has come up with a story of how decisions in this circumstance influence differential selective pressure. It seems that if you can't find a reasonably clear mechanism for differntial reproductive success, you should not bend over backwards to do so (that is, if it's that hard to find one, maybe it's because it isn't there).

My personal theory is that it stems from story telling and thus availability bias. Almost no story has the overdog as a good guy. This is probably the result of a story requiring conflict to occur in a non-predictable manner. Big, good guy crushes bad, little guy with little resistance is too foregone of a conclusion. Thus, every story we hear, we like the good guy. When we hear a story about Israel-Palestine (that happens to represent reality, roughly), we side with the little guy because, based on a massive compilation of (fictional) "evidence," the little guy is always right.

Of course, explaining the psychology of good stories is rather difficult; still, "side effect of other aspect of human psychology" seems more accurate than "result of differential reproduction" for something this specific, abstract, and practically useless. Though, of course, if someone comes up with a convincing mechanism for differential reproductive success, that would probably change my mind.