I have contemplated this particular thing for quite some time, and here is what I think (I am relying on a lot of assumptions though):
Money.
Voice-actors can be very expensive, and logically, what a voice-actor is paid should be proportional to how much work he/she does. In multi-route VNs, the only voice/text that you will hear/see much in every route is the protagonist's, something that would, according to my above assumption, be lots of work and therefore, cost a lot of money.
Then there is also the whole "blank slate" thing brought up in posts above mine...