Other than getting wet in the rain, I've never had any kind of damage to my bike from the road. I've driven to New Mexico and Vermont from Arkansas with bikes on the back of my Beetle. I thought about a cover, too, but I figured that would cut into my gas mileage so bad that I just didn't pursue it.
Covering the drive train seems like a solution. If you're worried about the rims like someone else said, you could put a wheel cover on with a hole poked through it for the skewer, I guess?
Karen
~~~~~~~~~~~~~~~~~~~~~~~~~~
insidious ungovernable cardboard