Actually the gov't workforce, and the military, have a "locality" pay. It doesn't make up the difference in the cost of living in those more expensive areas, but it certainly is a step in the right direction.
Of course airline pilots aren't necessarily forced to live in that high cost of living area like the controllers you speak of in your example. That ability to live in a different area than your work, for whatever reason - family, affordability, school, job, etc - and the ability to commute to work is suppose to be one of the perks of the job correct?