The towers, which hold the crossbars, sit on rubber pads on the edges of the roof, and they're held down by clips that fit under the side window gaskets.
It's always a good idea to wash and wax the roof before installing the rack system, and to put lots of wax where the towers sit. Then, when you put the rack system on, you want to make sure the rubber pads are totally clean.
With this approach, I've not had scratching problems on any of the cars I've used this on, (Audis and Subarus). HPH