A majority of people are uncomfortable with flying already, so horror movies based on the mortally vulnerable activity are especially horrifying. As someone who has had airplane disaster premonition dreams her whole life, I've been on dozens of crashes - all the way to the end - as a sort of psychic witness. Do I like to fly? Hell no! Every time I do fly, I think "what was I thinking getting on this machine with a stranger flying it?"
That being said, here's more fodder for that fear -
Flight That Disappeared: A flight with key people of importance is caught in a strange force.
Ghost of Flight 401: After a plane crashes, does it parts, reinstalled in other planes, bring a ghost with them?
The Langoliers: Based on a Stephen King novel, this movie deals with a plane flight in which sleeping passengers awaken to find the rest of the passengers gone and the plane landing at an apparently vacant airport. (on streaming Netflix now)
Twilight Zone: This trilogy of stories in movie form replays a classic "Twilight Zone" TV show episode in which a man is nervous flying and thinks he sees a monster on the plane's wing, causing great disruption of the flight.
Satan's Triangle: This 1975 movie of the week has a woman being rescued in the Bermuda Triangle by a helicopter to get caught in its mystery.
Airport: This 1970 movie takes an all-star cast in the air with a man meaning to take himself out and, hopefully not the entire passenger list.
Flight of the Living Dead: A substance on a flight causes passengers to turn into zombies.
Flightplan: Jodi Foster stars in this very tense thriller about a woman on a flight with her daughter and and her daughter goes missing and no one admits she was even on the flight.
Snakes On A Plane: Poisonous snakes are released on a plane to kill a witness and endangers everyone.
Final Destination: When teens get off a plane and it then crashes after take off, did they beat fate or is fate going to find them anyway?
Altitude: A small plane is taken under control of supernatural forces.
Murder on Flight 502: Farrah Fawcett, Sonny Bono and an all-star cast make this 1975 hip movie lots of fun. A letter left on a plane warns of murders happening on that flight.
Turbulence: Following a shootout on a flight, a stewardess must go up against a serial killer and land the plane.
Con Air: A transport plane or prisoners is taken over by the prisoners.
Flight of the Phoenix: Passengers on a plane that crashes in Mongolia, rush to try to rebuild the plane and get out.
Die Hard 2: An airport is held hostage and planes not allowed to land.
Air Force One: The president's plane is taken captive and he is going to work against them to save his family and those on board.
Panic In the Skies: A plane struck by lightning is assessed by those on board who think autopilot would land it, but those on the ground aren't certain if they should just blow it out of the air instead of letting it crash into the homes below.
Nowhere To Land: A hijacked plane might have a biochemical device on board and no one wants them to land on their tarmac.
There are a LOT more airplane horror movies, but I think I've given you a good mix of hostages and supernatural, crazy events and bad weather to make you quite uneasy.