Hello Greenie,
I often worried about this. I too ride a lot and have taken my D5000 with a couple of lens and a flash unit on several long trips. I have a Road King with hard bags and haven't had any issues. I carry the camera, lens, and flash in a small Nikon bag and make sure it's packed tight. I also make sure the camera bag is packed tight in the saddlebag to limit movement, wrapped in sweatshirts, jackets, whatever.
I suspect that vibration is not a good thing, but I haven't had any issues yet.
Enjoy the ride and be safe out there ... it's not the destination, it's the journey.