Most of the trunk mounted bike racks have rubber mounts for the bikes to rest on, so scratching isn't a problem for the bikes (unless you mix different kinds of bikes and one of those bikes has weird geometry). The scratch on my car came from the toe cage on my friend's bike...I have an older car with more of a pronounced bumper than most cars these days seem to have, so I think that is part of the reason the toe cage rubbed against the car.