That's because they *are* breaking even on actually flying airplanes carrying cargo, whether it be breathing meat-sacks or crates of plastic shit from China.
The profitable airlines either are charging more for their tickets and delivering higher value through entertainment options and comfort, or co-branding credit cards and operating the aircraft as a loss-leader to getting you to spend as much as possible on the co-branded credit card, so that BofA / Chase / Amex pays them, and it's pure profit.
That's why Delta is leading the way in profitability - they cranked up the SkyMiles benefits a few years ago in a way that encourages you to use that Amex as much as possible, and Delta gets a taste of every single dollar spent on that card, whether it's on air fare or not. This allows them to "invest" in lower prices that aren't that much above the budget guys, but with more comfort / value and a much larger network to utilize to get where you are going without shitty red-eye flights or 4-layover bullshit routes.
Now Alaska, American, Southwest, and United are following suit; it's the only way they can compete on price and not go bankrupt. And the low-fare guys that started the prices trending downward? They don't have those cards, so they're fucked. Expect Spirit and Frontier to be distant memories in the next 5 years unless they change their tune, and fast.