There was an article in a dutch bike magazin a couple of weeks ago. It stated that putting a carbon bike in on of those car bike transporters is a bad thing. The carbon fibers are made to sustain a force in a specific direction (the bike direction) and those bikeracks often have some contruction where an arm is fixated around a tube. This is not good for the frame.

-However- if you can fixate on a non carbon part of the bike (like the seatpost) then the problem is eliminated.

I put my carbon bike in the back of my car with some blankets under and over it.