I'm pretty convinced this all boils down to a sort of low-grade white collar corruption: people who travel a lot for business sometimes can get away with favoring one airline over another, where this decision costs the shareholders a little bit but only the employee who's traveling will notice. Then it makes perfect sense: the employee directs a little extra money from the treasury to the airline, the airline provides a kickback to the employee in the form of a little comfort or attention, and that explains the whole miles phenomenon.