The exact same thing happened to us, only the bus that finally arrived was NOT for our pickup, but for the next pickup. We were fortunate, though, to have a GREAT driver. When he heard that our bus had not shown up, he radioed in and got premission to take those passengers from the earlier pickup. Our bus wasn't full, so we were able to take about half of the next pickup too. The driver radioed again and let them know there were still (X) amount of passengers waiting, and he told them the next bus was only a few minutes away. By the time we got that straightened out and got everyone's luggage loaded, my family was starting to stress big time (and I'm sure we weren't the only ones).
On our way to the airport the driver assured everyone that they wouldn't miss their flights. Then he proceeded to find out who had the earliest flights (that would be us), then explained to the rest of the passengers that he was going to stop first at SouthWest and let us off, or we would miss our flight! And he did! We were so pleased with him, we really, really wanted to give him a tip but he wouldn't accept it. Our last little bit of pixie dust from our WDW trip!