First of all, it's a Jeep. It's not happy unless you're cruising around in the middle of the woods somewhere. If you're scared to get your Jeep scratched, sell it and buy a freakin Miata. Ok, now that I got that out of my system lemme help ya out with those scratches.
After a recent off roading excursion in the Jeep we ended up on a pig trail that was REALLY bad. This is what I hope to help you guys avoid. I don't mind scratches, but honestly this was a trail I wouldn't have rode on a bicycle and we didn't have anywhere to turn around for a good while.
I found a product called Mothers Scratch Remover and it really helped a lot. It seems like it gets down in the scratches in the clear coat and fills them up. Highly recommended. I really wish I'd taken some before and after shots, but I'm dense so you'll have to take my word for it that it works well.