We don't know what happened beyond brief phone calls and cockpit voice recorders. However, it is the director's job to analyze the event to the best of his ability and create his own personal interpretation.
I was very impressed with the director's decision to have the hijacker flying the plane begin flying erratically as his final defense to keep the passengers out of the cockpit. I had not thought of it before, but that would have been the rational move on his part. A lesser film would have missed that.
Any thoughts on Greengrass' decision to have the hijackers speak almost no English? It intensifies the us/them dichotomy of the film. But I wonder whether this is based on his research of the hijackers or a directorial decision. The hijackers do not even know enough English to shout "sit down" at people.
The erratic flying is solely based on fact. The cockpit recorders record not only voice, but control stick input. Every movement of the controls is recorded by the cockpit computer, as well as gauge readings such as altimeter and rate of speed.
Those readings can then be loaded into a program which creates a simulation of the plane's flight up until recording stops. When the flight was recreated, it was shown that the plane went into a steep dive with contant banking movements to the left and the right. The hijacker, clearly knew the passengers were rushing the cockpit and attempted to knock them off their feet. In the end, the plane banked until it was on its back and then began a plummet near the speed of sound into the ground.
I think it was a decision to drive home that the Islamists are an alien culture. There was no BS sympathy for the hijackers point of view. They are just psychotic killers.
I don't expect this film to play well in Muslim countries