I have scratches on the side from people feet. Really started to scratch away the paint. Its on the drivers side though so its my fault, I figure its no worse than the other scratches. This was with the stock diamond plate rubi rocker guards. They come about half way up.
I do have rocker guards on the side that cover all the way up to the door (thus no more scratches). However I pulled them off today to repaint them since the paint it starting to come off (the paint didn't adheare well in the winter when I put them on). Anyways they have eating through the paint in areas.
Places do sell this plastic striping you can put on the back of the sliders to keep the water from getting in. I had these when I had the rubicon stock guards. They didn't keep the water out, and the paint still got messed up. It is duller and faded where the plastic rubbed against it.
Either way if you put something on the paint well be messed up underneath. Not to mention you have to drill numerous holes to mount these things, so no going back.
Personally I like my rocker guards, but I use them for functionality purposes. Wish I had them to begin with so I wouldn't have this nasty dent in the side.
Some people use silicon caulking, etc to seal them up, not sure how good this works.
2004 Black Rubicon w/ 5 spd
RE 3.5 SuperFlex & Front Trackbar / JKS 1.25" BL & MML / 35x12.5 MTRs on 15x8 AR-23s / Currie Anti-Rock / Jeeperman Bumpers / Rokmen Sliders / York OBA / Harbor Freight 8k Winch