It somehow feels more natural and logical to stick with a ruling that all creatures, mount or not, are not allowed to fly while carrying medium or heavy load (or wearing medium or heavy armor).
Just imagine this:
An eagle (Str 10, weighs 8-15 pounds) takes off while carrying a 100 pound deer?
Also:
A pegasus could fly at his maximum load (Str 18: 300 lbs.) but not when it carries medium load (101 lbs.) while a halfling (30 lbs.) is using it as a mount?