Commercial airliners fly over or around thunderstorms when cruising, and even when passing through storms thunder is not audible within the cabin.
They are flying in a US Commercial plane, and the secondary pilot kept answering the microphone flight deck when speaking to the back of the plane. The front the plane is actually called a cockpit. The term flight deck is where you would land a US Naval plane or a US Naval plane would take off from when it is out at sea on a US Naval ship.
When the plane loses power and goes into a dive, the pilot flying says he has "dual engine failure", even though the aircraft in the movie is clearly a 3 engine Boeing 727-200 aircraft.