Is it because typically during these long flights there is a a change in multiple time zones and that messes your circadian rythm?
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>Is it because … there is a change in multiple time zones …?
Yes. I can personally attest that flying from Anchorage, AK to San Diego, CA (7 hour flight; 1 time zone) is essentially painless on arrival, while flying Chicago to London (half-hour longer flight; 6 time zones) will leave one shagged out for days.
Distance traveled on 20hr train ride at 50mph average = 1,000 miles (about 2 time zones)
Distance traveled on 14hr plane ride at 300mph average = 4,200 miles (about 6 time zones)
The US Navy has done a lot of research on flight fatigue, and a lot of it comes down to the tiny stabilization movements we are constantly making while in flight. These tiny muscle movements add up, and contribute significantly to the overall feeling of fatigue after a flight.
Commercial jetliners have the cabin altitude pressure set to 8000ft. This fatigues the body faster then you would lower normal altitude on a train. Private jets can get cabin down to around 3000ft in some cases and have improved experience and less fatigue for passengers there.
Many answers have mentioned time zone change, but another factor to consider is the pressure and humidity during the prolonged period an airplane.
In a typical passenger aircraft, the air is very dry and the air pressure makes it feel like you’re sitting at around 8000 feet elevation for most of the trip. (Newer aircraft like the Boeing 787 and Airbus A350 do a bit better on both of these.)
That will have an effect on how you feel, especially after several hours.
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