It's complicated but it basically goes like this:

The revenue from each passenger is spread out across the miles that they fly for a particular ticket sale. So you pay $100 to fly 1,000 miles that means the airline nets 10 cents per mile. You might do 300 of those miles on one leg and the other 700 on the other leg. One leg is credited with $30, the other with $70. Now multiply that out by the other 200,000 people UA typically flys in a day, and keep historical data for each leg flown by the airline for each of the 365 days in a year and you can begin to see how they "know" wether a route is profitable or not. You can do the same type of thing for expenses, some are fixed, such as a monthly lease payment and some are not.

That is the five minute version of something that takes years and years to understand and even then the revenue side is managed by some of the biggest supercomputers known to man.