We used the Busch Gardens shuttle transport in July with our DS who also uses a wheelchair.
You need to call 1-800-221 1339 and book this a few days ahead and let them know you have a wheelchair user in your party. If your DS can transfer onto the coach you could travel in that and fold his chair, but if he needs to travel seated in his wheelchair they will accommodate your party in a smaller wheelchair accessible van.
We found the service absolutely fantastic, we caught the shuttle from Seaworld at 9am. They laid on a wheelchair accessible van just for us and our driver, Tom, was so sweet and helpful. He dropped us right at the park entrance and picked us up there too, arriving early in case we had had enough and wanted to leave then. We had an awful journey back to Orlando due to the effects of hurricane Dennis, but Tom was fabulous telling us what to do if the hurricane hit near us and offering to drive us back to our hotel rather than have us driving back from Seaworld in the terrible storm.
I would definately use the service again.