You could say more or less the same things about your mathematical intuitions: they come from one or several modules, evolutionary psychology can explain how these modules arose or were pressed into service for mathematics, and we can readily write program to extend these capabilities.
Yet there seem to be some mysteries left over in math, for instance finding from time to time some deep unifying principles, such that topics which previously appeared entirely distinct turn out to be facets of a single theory. Philosophically, there are questions such as the debate opposing mathematical realism and anti-realism. There are questions of the elegance of theories being a subjective or objective matter, and so on.
lukeprog gave a list of metaethics questions here:
Most of these questions make no sense to me. I imagine that the moral intuitions in my brain come from a special black box within it, a "morality core" whose outputs I cannot easily change. (Explaining how my "morality core" ended up a certain way is a task for evo psych, not philosophy.) Or I can be more enlightened and adopt Nesov's idea that the "morality core" doesn't exist as a unified device, only as an umbrella name for all the diverse "reasons for action" that my brain can fire. Either perspective can be implemented as a computer program pretty easily, so I don't feel there's any philosophical mystery left over. All we have is factual questions about how people's "morality cores" vary in time and from person to person, how compelling their voices are, finding patterns in their outputs, etc. Can someone explain what problem metaethics is supposed to solve?