Making money with airplanes shouldn't be that hard, if you charge for what the service/product costs. If an airline with 1,500 flights per day, arranged fares such that they averaged a profit of just $2,500 per flight, which would not increase fares too significantly, that airline could make $1,368,750,000 per year. Instead, you have flights that profit $200, while others lose.
If it costs $28,000 to operate a flight from JFK-LAX, between fuel, labor, etc., and an 8AM departure averages 100 passengers, bare minimum should be $280 per person to break even. Obviously breaking even isn't what you want to do; you want a profit. If your goal is to average a profit of $2,500 per that flight, over the course of a year, you should charge a minimum of $305 for that flight. I also think airline should do away with the one person paying $100, while the person next to them pays $800. The airlines might fear they will turn the $100 passenger away, when they have to pay $305, but I disagree. The person who would normally pay $800 will jump at the $305, and thus it evens out. Also, people are all about the convenience factor. $305 is still extremely cheap to fly across the country. Not to mention you would probably pay that in gas trying to drive that anyway.
The airlines could do a little research, determine the average number of passengers per flight, per departure, per time of the year, and arrange fares to average a certain profit per day, over the course of a year, for that flight.
I also think something needs to be done about "round-trip" airfare. If someone buys a one way ticket from ABC to DEF, it costs $700, but if they get a round trip ticket, it costs them $300. I say if it costs $305 to fly from JFK to LAX, and you want to come back, you pay another $305. That is still just $610 for a round-trip, cross country flight. Still not that expensive, considering what is involves (someone flying you across the country).
The above may be a little over simplified, but in theory, it would work, if all of the airlines would do it.