So you're talking about the cost of the gas on one half of the trip. How about all the employees it takes to get you from point A to point B plus insurance which is in hundreds of millions for liability, the overhead in facilities to accommodate passengers, plus landing fees, plus maintenance. And then there is the lease or ownership of the airframe and engines. Do you know much a battery on a small GA airplane compares to the cost of a battery in a car? Take any car part multiple it's cost by 10 to achieve proper FAA certification. And that's comparing an auto to GA airplanes. Any new part other than replacing screws or likewise in a modern airliner is minimum $10,000. It's not landing on the moon, but it's making popcorn either.
There's a reason the list of airlines over time that have ceased business and or declared bankruptcy is far greater than any other industry besides independently owned restaurants. $1100 RT coast to coast is a ripoff if you're of the Yugo mentality.
That's the nature of the business. My assumption was coach class. First class roundtrip is in the thousands. The airlines can make money on transcontinental flights, and many do it well. You are detracting from the main point, which is that UniCal had a monopoly on the nonstop SFO EWR market and therefore charged very high fares. Now that VX came in United not only matched the fares, they doubled daily frequency. United isn't going to make money on that route as they used to before, and doubling capacity is going to hurt them.
As for the other points you made, wages, insurance, liability, fuel, all that is accounted for in the airline's finance and revenue managment department. $1100 roundtrip is still too much. I've found cheaper fares on other airlines for that market, but with a stop. Again, UA charged a premium for that route because they had a monopoly.