The only way to prevent damage under a flare is to put something under it to protect the paint - linex, 3M or other. I've got Mopar flares on the 06 and they look nice but dirt collects under them. Wish I had just linex'd them when I did the rockers. On my 01, I used Al's liner and did the bed, rockers and fenders. It was a pain to tap but looks good. On the 2nd gen. , the fender has a lip you can use to tap a good line. Not there on the 3rd gen. so you'd have to free hand it. I'm not that good and I doubt my linex guy is either.
On my brother's 06, we did something different. He bought it used and it has those ugly chrome flares. We had those linex'd with the rockers/bumpers and it looks really nice. Nice accent, subtle and not too big or flashy ; very unique. These smaller flares don't require a huge tire to look right either.
Unless you want the look of a flare, I say go linex. Shop around, price can vary considerably.