I use paper towels because I keep my snakes in a rack system and it just made more sense. Plus, I like that I can see anything they leave behind (poop, urates, regurges, etc) without having to dig it out or pick bedding off it.
A lot of people use Aspen (shredded or flakes), Sanichips, Reptile carpet, carpet fresh, or coconut bark. If you choose to use a substrate, consider feeding outside the viv as the snake *might* ingest the materials (Aspen, sanichips, carpet fresh, bark). I've heard sanichips don't hurt them, but don't know first hand. Aspen and bark can cause impactions. I honestly don't know that I've heard of anything one way or the other with carefresh. Obviously they can't exactly ingest the reptile carpet...
The people who use substrates either use the burrowing reason for using it or the fact that it's easier to spot clean (you can just pick up the clumps kind of like cat litter).