For small insects such as flies, air is a relatively thick and viscous fluid*. The air in the bus is, on average, moving at the same speed as the bus and is likely to accelerate the fly to the speed of the bus before the rear window of the bus can reach the fly
If we are measuring speed with respect to an observer standing still outside the bus, the observer sees the fly moving slowly (1-2 m/s) adjacent to the path of the approaching bus, as the fly is sucked in by airflow through a side window, assuming it misses the edge of the window frame, the fly is accelerated to the speed of the bus (10-20 m/s). It may later choose to land on any window (so you can't say it will never choose to make contact with any specific window)
* It's more accurate to say the viscosity of air becomes a dominant factor in the flight of flies, much more so than for the flight of pigeons or planes.