Within software at least, there are simply more people that have significant 'clock time' working within well run software companies in San Francisco, Seattle, Austin, etc.
It's no different than college football players that spend their four years in well run systems that run pro style offenses. Sure, there may be a kid that has insane athletic ability that is playing at Calhoun Community College, but someone like Jerry Juedy ( wide receiver for Alabama ) is the player that the Denver Broncos will choose if they can get him.
There simply aren't as many well run software companies in Omaha as there are in Seattle. And one could argue that the best free agents are going to be the ones coming out of those cities who can command higher market rates because companies believe there is higher ROI.