The locations aren't a coincidence.
-The culture in SV is very much centered on scaling quickly and taking a bunch of VC money to do it. If you're in Chicago or Atlanta, there's not that same sort of culture.
-Unless a company spends a ton of time in California seeking VC money, SV VC's aren't going to get to know companies outside of SV. There's already so much activity right on their doorsteps that there's little incentive or time to go elsewhere. Even ycombinator, which accepts applicants worldwide, makes applicants come to California to interview and work.
-The VC's that exist in other places don't usually focus on software/internet space like SV VC's do.
So founders outside of SV, NY, and Boston act more like they're starting a restaurant or a clothing store. They expect that they'll have to quickly build a profitable business before expanding too much. Nobody is going to say to a first-time restaurant owner, "We'll expect that your first 20 locations won't make any money, but once you get to 100 we'll all be rich."
(The economies of scale in software are different than restaurants, of course, so there's often valid reasons for software companies to expand as quickly as possible, that's just not an option without lots of outside money.)