We had a client today make a strong statement about having an aero wheel on a car-rack – it is best not to do it. His bike was mounted via a hitch rack behind the car, with this aero wheel.
There is too much cross-winds for it too be safe. This accident not only destroyed his wheel, but also, his frame. The bike flying off his car (which he saw via the rear view mirror) caused his saddle to shear off the seatpost and crack his seat stays.
The best/safest thing is to have a spoked non-aero wheel on your bike for traveling, then put on the disc wheel before the ride. It sucks to have to swap the wheel out, but that is better than having this type of accident happen.