Why would a culture be matrilineal? (This question may not seem important, but go read Avunculocal residence. You'll start to wonder). Matrilineal societies don't usually give more power to females, so why determine descent through them?
There isn't one single answer for all societies, but in some cases the answer is simply that the babies come from the mother's body. In some cases, the father isn't seen as having anything to do with the creation of the child.
If you know another explanation, please post it.