Besides erecting up a straw man who believes in utopia, the pseudononymous Yeti asserts that tolerance is not natural. This is understandable: sociobiology, evolutionary psychology, selfish gene theory, and other attempts to understand human nature indicate this on the surface: it is only in our interest to permit the existence of others who are our kin. This is exactly the viewpoint I was countering when I ruffled feathers asserting that difference need not threaten.
So why do I believe that tolerance can arise naturally, when not overridden by threats? First, recent Western history seems to support the thesis. As wealth reduces the competition for resources, differences in gender, skin color, religion, and sexual preference have become increasingly acceptable. (Whether you believe this is "progress" or "decay" is irrelevant to the observation.) Moreover, both simulation and theory have supported cooperation outside recognized kin as a natural behavior over the last 20 years of study.
Perhaps most compelling to myself, I don't personally feel the need to attack others who are different than myself for that reason alone. Only when they act against me do they evoke my ire, and even then I am slow to group everyone who looks like the guy who hit me into the group that must be annihilated.