I look at things like this just like sales (car, clothing, etc). For instance, a brand new car. The dealer/automaker has a bare minimum price you will never see, which is what the dealer pays the automaker to put that car/truck/SUV on the lot. Sometimes that is paid for by a dealer loan. Then, they put a sticker on it with the MSRP. That gives the dealer some profit. Like right now, dealers need to get rid of their stock, so they bring down the price by thousands. They still make money, just not as much. That is also why dealers have begun using "no-haggle price", it is not to prevent headaches, it is to lock in their profit!
In terms of hotels, being that my father-in-law worked at hotels in the Boston area for years, we know there is an absolute minimum. Usually, they charge that amount to employees. When my wife and I were married north of Boston in 2009, our "first night" was at the Hampton Inn @ Worchester MA. Since her dad worked there (he was a night auditor), instead of the usual $150+ per night, we got it for $30. If a Hampton Inn has a "break even" cost of $30/night with 50 rooms, they must make $1500/night average (an example). At $150/room, if they average 10 rooms occupied for a month, they're doing OK.
Since airlines make HUGE profits with baggage fees, they can afford to drop the prices for certain groups like COSTCO, as well as paying travel websites to advertise better prices.
TS