I'm not aware of entire movies being rejected, but scenes can get deleted. This happened with "Rain Man". From Uneasy Airlines Get Final Cut on 'Rain Man'
Passengers on at least 15 different airlines have been treated to
Dustin Hoffman and Tom Cruise's Academy Award-winning road trip in
"Rain Man" since the beginning of June, but the crucial scene that
propels them on their highway odyssey in the first place has been
edited right out of the picture.
"I think it's a key scene to the entire movie. That's why it's in
there," Levinson told the Associated Press. "Without that scene, it
comes down to this: You basically lose an enormous impact of the film.
That scene tells you that they, mechanically, are forced to drive
across country and, secondly, that Charlie can only push Raymond so
far because he knows what will happen."
And at least a passenger organisation (not an airline organisation) has guidelines about this. From Curious cuts to in-flight films
The Airline Passenger Experience Association sets out a quick
checklist of standards of what’s considered appropriate mid-air
viewing: “No airline crash scenes or references to airline disasters;
caution in depicting or referencing terrorism or; no nudity/sex
scenes; no profanity; no racist comments or denigrating references to
cultures, religions, or nationalities; caution in depicting violence,
drug and physical abuse.