A few reasons. First of all, think of the horror that is concert seating. One they became a tradable commodity, large firms started buying up huge blocks of seats and then reselling them. Other organizations, such as radio stations that would give out prizes bought up the best seats right away. So if I wanted front row center, they were gone. Short of winning the contest, even if I had money in hand I would be unable to get those seats.
So if they allowed unregulated, gray market resale of seats, here is what would happen...people would go into the business of buying seats up. It would be the best ones first of course..exit rows, etc. At their large volumes, they would get top tier status quickly and before you know it, your ability to select those seats as part of your status would be useless. They would be gone the second the flight is open to book. You would end up having to buy from these brokers, and yeah you would be paying alot more.
Do the airlines care about one off's onboard between people? No. Do they care if I tell a swap requestor I want 100 to swap? No. But if you could buy and trade on the open market..then yeah, they would take notice.