Yeah, I tip them. It's mostly that if I plan on using that shuttle service again, I don't want them to take their time and making me wait for the ride because I didn't tip the first time. I'm sure the hotel pays them, but no idea how much.
I usually tip $5, but I've never really taken one more than 5 miles or so, which is about the limit that most shuttles will even run. Definitely less than what cab fare would've been.