I had this same dilemma a few days ago.

Your roots will undoubtedly get much longer and if you dont do anything they'll be exposed and susceptible. Some people don't have a problem with this, but I didn't like the idea. Coco Matting is an option: http://boards.cannabis.com/showthread.php?t=96478.

rockwool would hold too much water, i've seen other people use hydroton for your problem though. what's in your netpots?