Yes, they did. In fact I did the one time I stayed onsite. But that was all just a drop in the bucket and even if they did it didn't save them money they still had to maintain the scheduled runs. Believe me they couldn't have made it work without a regular schedule set up. They may have not published what it was, but it was there. So it cost a fortune to operate those buses. The charge for parking was more of just a telling story of how little Disney cared about its most profitable Guest.
A resort that charges that much for a room and isn't in a city where providing parking is a huge expense is just taking them for a ride. However, if they foresaw the ending of the bus thing than logically there would be more people renting cars and needing to park. To me that was the telling point. They had no need to charge for that, especially considering how much they charged for a room, but it was done for a reason and it was to make that change and eliminate the Magic Bus. There were two possible scenario's to that decision. The first was that when they did stop the bus service people coming in from a distance would either have to rent a car, taxi in or find public charge transportation. Since some amount of money was required anyway, many would elect for the car and then not only would they stop having to spend thousands of dollars to pay for the operation of the Bus, but could increase revenue by charging for parking.
They might even have considered that there would be backlash and could eliminate the parking fee but still save the big bucks on the bus service. We haven't seen that restored yet have we? I doubt we ever will but the gift of free parking shows that Disney cares about its guests and they slack off with the complaints. They then become just like any other theme park that you have to find a way to get too. No harm, no foul! Modern times made it easy with things like Uber and the like that the idea of being able to leave the resort for other entertainment venues became a whole lot easier, so the bus was a waste of money.