Mass and volume both count, in an aircraft, don't they? And many oversize humans present logistical and safety challenges:
- Taking up more than one seat with girth, needing a seatbelt extender.
- Fitting through narrow passages, tight turns, limited headroom
- An unconscious person may need to be lifted, and transported somehow
- Toilets and life vests and other safety equipment, rated for your "standard average man size"
- Total mass of passengers/cargo, and its distribution on the aircraft itself
Elevators in the US have a maximum weight and maximum occupancy rating.
Arguably, if obesity is a disability, then appeal to the Americans with Disability Act or similar regulations, but from a standpoint of safety and the common good, it does not seem unreasonable for airlines to charge extra to cover their expenses above.
