I think that's a good question. It is natural to require that the total charge in the universe was zero at the start of its life (same goes for all quantum numbers). Otherwise, there was something before there was anything! Seriously, either this matter-antimatter asymmetry was an initial condition (in which case we can't hope to understand it) or it appeared at some point during the course of things.

The problem of finding the exact mechanism that gave us the matter-filled universe we observe today, with all the antimatter gone is an open question. There are a bunch of hypotheses, and experiments coming son to a large hadron collider near you will help physicists gather pieces of the puzzle.