As for ethics of this topic, I think the quoted government response about one such case is spot on - this is people acting in bad faith. Whether or not you think it's fine to act in bad faith depends on to which group you subscribe - defectors, or cooperators.
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EDIT: The article would make a much stronger point if it focused on the problem of "hidden city" tickets, where people choosing to reduce their travel costs are not just haggling over price, but breaking a deal and wasting airline's fuel.
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EDIT2: Took a shower, thought about it some more.
My initial paragraph isn't about airlines really, it's an observation made after seeing a stream of comments arguing for general selfishness.
As for problems with some of the travel "hacks", I have issues with two of those in particular. "Hidden city" flying is one, and using golden-card-carrying third party to buy you tickets is the second. Both of them introduce waste - the more people do that, the more often a plane flies with seats empty, wasting fuel that could otherwise provide utility by carrying other passengers. And speaking of other passengers, this is another thing to consider - if you use a travel "hack" that leaves an airplane with an empty seat, you're taking away the seat from another traveler, who could have used it. Or, given the discriminatory pricing, who could have paid less for it. So by using those kinds of tricks, people are not only hurting the airline, they're also hurting each other.