When I was a CFI, we would charge students for the time they put in their logbook. Of course, that technique is a little bit more tricky with renters. The industry default appears to be airborne time plus 5 minutes either side. You then fall into the trap of renters rushing on the ground.
I once considered a fixed rate/hour plus a rate for fuel used, the latter being a rough interpretation from tacho. The advantage here would be that renters wouldn't be racing around at 2500rpm all they time. Unfortunately, that idea proved too difficult to manage.
Back to the OP, I think it unethical for you to be charged engine running time when not taxiing.