Although the A/C system itself will continue to work with the window open it won't be as effective. The purpose of an A/C system is to remove humidity from a room (i.e. passenger compartment), and an open window is constantly reintroducing it back into the room/passenger compartment. It won't effectively cool with the windows open, since warmer air is going to be constantly going into the vehicle via the windows.
You get that, dummy? You want to stay cool on the bus?
LEAVE THE FUCKING WINDOWS CLOSED WHEN THE AIR CONDITIONER IS RUNNING!!!!
-TOO HOT TO BE COOL