There are Nikon lenses out there that do not have any motors in them. My Nikon 50mm f/1.8D is one of those. For some reason, I was surprised that it didn't autofocus on my D5100.
Then there is also the argument that if the VR was built into the camera body, you could get lighter, less expensive glass. Seems like VR on the camera is such a compromise for different lens types, etc.