While not to disagree with Wino, there are a couple of other issues missed.
First, during the bankruptcy years of 2002-2006, United and USAirways gave major discounts to Apple Vacations in order to secure income. Remember they also sold seats to the general public at super cheap rates during this time as well. Word is those super discounts are now disappearing
The second factor is the "bargaining chip" factor. By having their own airline, Apple is able to use that as a bargaining chip when negotiating ticket prices with other airlines. I don't know for sure, but word around the company is that in that respect alone USA 3000 has been financially beneficial to the Apple group even if the airline doesn't make a profit operationally.
Again this isn't to disagree with Wino, simply pointing out a couple of other factors.