I have a roof rack (Yakima Sprocket Rocket). We initially tried a rear rack (can't remember if it was Yakima or Thule) but returned it because shaped carbon tubes did not fit into it very well, leading to a lot of sway that would cause scratching from the rack itself and would risk scratching if more than one frame were placed on the rack because the poor fit increased movement.
I really like the rack I have, actually. It's super solid -- if you put a hand on the bike, the bike doesn't move at all, but you can rock the car. I also bought the lock set, so not only does the skewer lock, but the rack itself locks onto the factory install roofrack with keys. I still won't really let the car out of my sight for any length of time with bikes attached (I heard a horror story of a thief actually removing the factory installed roof rack and making off with two custom sevens worth more than the car they were mounted on). But I feel totally safe driving with the bikes on the highway -- with a rear rack I was always worried either that we would get rear-ended or that sway (from sudden turns or slowing, from bumps, or just from wind) would cause frame damage and scratching (we usually have two bikes on at a time, so as mentioned above damage could occur between the frame and the rack or between the two frames).
The style roof rack I have requires removal of the front wheel and clamps the fork in front and the rear rim in back. I talked to several people in different LBSs about this style rack and all of them assured me it was safe for carbon frames. Then again, I also put my carbon bike in a trainer in the winter...



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