I have no idea how many people get on the plane or what size plane is used, but I would think the flight would be full. Commercial aviation starts boarding the bigger planes nearly an hour before takeoff, it's a slow process. So getting off the bus at the airport, moving all those people and their stuff from the bus through the airport and onto the plane would take an hour at least. By the time the plane finally gets in the air the busses could easily be an hour and a half to two hours down the road. Getting off the plane on the other end usually goes much quicker, but at best 30 more minutes to go from the plane to bus. I'm sure the plane is still quicker, but not by alot.
Someone also mentioned that airplane seats are more comfortable that tour bus seats. My experience is very different than yours.