Stobbo is right, Thule is pricey.
However since I didn't know any better at the time, that's what I have
I bought removable crossbars that clip into the door frames. I had them for my Toyota Matrix and then re adjusted them to fit on the Mazda when I traded up. I always had foam pads that wrapped around the bars, they were a gift from the kayak dealer when I bought the first Hobie. You can achieve the same effect (on the cheap) by sacrificing a pool noodle and cutting a slit in it so you can enclose the crossbar. You will want to zip tie it in place though, because it will not stay there on its own.
I load my kayaks from the sides or the car, lifting them over head, so no rolling on the bars for me. I think you will probably get a few scratches here and there when loading them, but its all superficial and doesn't affect the kayak much.