I put a sock under the part that sits on the trunk and it's actually done a pretty good job of protecting the paint. I wish I had done that for the first few months I had it on the car. I think you can protect your car's paint somewhat, but it will get scratched no matter what I'll bet. Except for long trips, my rack stays on my car all the time. I don't drive a whole lot anyway, but it's just easier to leave it on. It probably hurts the gas mileage a bit, and after 4 years I've noticed that the straps are getting a little dry/brittle probably from being in the sun a whole lot. If I had to do it over again, I'd probably take the rack off and only put it on when I need it (but that's kind of a pain for me).
BTW- that looks like a really nice rack. We bought the much cheaper Bones and have never worried about it being cut from the car- and we've traveled around the country with our expensive racing bikes on it (we can lock the bikes to the rack, but the rack doesn't lock to the car). I figure if they cut the straps they have a whole lot to cart away- the rack with both bikes locked with 3 locks to it. Good luck.