Well that fee is what pays for points/cash back. So although they're not literally taking them, they are taking the fees that would have funded them. So they are in effect taking them.
You stand between the carnival operator and the riders holding up a curtain so they can't see each other. In exchange for this anonymizing service you take a 1% cut of each transaction, then spend it on a ride yourself at the end of the day. The 1% cut is priced into the operator's ticket prices so they still make enough profit, and is practically invisible to the rider, but if the service did not exist, then the tickets could be sold 1% cheaper. This is the model, whether or not you call it "taking" the 1% or "adding on" the 1% is inconsequential.