In most cases, it will clarify with the source of the flight. For example, the Fly spell allows you to move at speed 60, or speed 40 if you're under a medium or heavy load. This means that a burly wizard (Strength 30) can probably carry a fighter in both hands, where a regular wizard (Strength 10) would not be able to.
I could swear that I've also seen some creatures which can only fly when unencumbered, but I can't find any examples right now.