Yep, they run until the park is clear. If you happen to be one of the last out, they "might" combine resorts, but they will get you there.
Also, if you want to go to another park, the bus going to the TTC will run continuously until the last park of the day closes, so you can take that bus and get to any park from there. (I found this out last trip. A bus driver told me those run because somebody just about every day will leave their car parked at for example, Animal Kingdom which closes at 5pm and take the bus for example, to MK which closes at midnight. So they provide the bus back to Animal Kingdom from the TTC to go get their car.