An interesting point, but I think there are some other subtleties here that are going unnoticed.

If we look at this from the standpoint of transactional analysis (and contextualize this narrative from the airline employee's point of view), this becomes less of a morality tale than a mini-drama about struggle for power. Two facts about airline employee's lives are relevant: 1) Their jobs place them at the low end of the socio-economic ladder, and 2) they are constantly exposed to and subservient to people with the financial means necessary to purchase air travel to distant locations. If this isn't a recipe for Nietzschean resentment, I don't know what is. Airline employees are prostrate before the abuses of the elite, and so subtly struggle to throw up obstacles to the elite's success, if only by causing irritation. This obstruction is best dealt out to the most egregious abusers, not only because it 'trains' the elite to respect the servers, but also because it gives the veneer of morality to the action.

What if, for example, the story had been told from a different angle? Two airline counter employees each receive asshole customers. One of them responds in kind, and the other responds with kindness. The 'in kind' customer escalates, but the 'other cheek' customer settles down, apologizes, and--the icing on the cake--the 'other cheek' employee gets him booked on a choice flight or provides some other bonus? Who knows, maybe the 'other cheek' employee gets promoted to supervisor, with attendant pay increase!

So, we can see that the 'nice deed' garners some benefit for the doer. This at least opens up the possibility that it is a crass manipulative move on the doers part. (Indeed, in the story in the article, the traveler not only received the earlier flight and the good will of the attendant, but also got to smugly refer to his friend as 'such an asshole' and got to gloat to his friend's face!)

Also, though we see that there is a crass benefit to the doer of nice deeds, the story is presented as a morality tale, as if the nice deed was done for the sake of niceness, but with the attendant trifling success of having incidentally, almost by accident really, attained some material good, which, it just so happens, was in the control of the gatekeeper-recipient. As if the passenger regaling us with the tale would continue to be nice, for example, even if so doing would only serve to invariably further enrage the surly staff at every encounter.

I'm not holding up unconditional niceness as an ideal, but I think it is important to recognize the full dynamic before reading too much into the situation. Nietzsche, for example, said that the Ubermensch could 'call a man his enemy without calling him evil.' In this instance, that would probably consist of recognizing that both passengers and airline employees feel powerless, and strive to master the situation with various tactics, not least of which are surliness, rudeness, and/or niceness. This is, fundamentally, a recognition of the amorality of the actors and their actions.

In a lot of ways, this is a fundamental realization that successful customer service organizations must realize, even if they sublimate it. They simply have to remove the moral indignation portion of their interactions with customers and say, "By acting in a certain way, even if we lose out at the level of the interpersonal morality play, we receive the most benefit for ourselves. Further, the only thing that keeps this from being overly crass is that we realize our personal benefit by creating the best outcome for our customers. After all, every dollar we ever hope to earn is in someone else's pocket."