depending what you want yours to look like I have seen flares with a bedliner or rockergaurd material on them. I actually like the look of it, rough but it looks different which is what I like. I would think you'd want a more rubberized rockergaurd coating, as opposed to the stiffer bedliner stuff.

97xj 4.0L cold air, Banks, Flowmaster Exhuast, 99 intake, 4.5", 33's