finance -- New York, Boston automobiles -- Detroit entertainment -- LA etc.
There are natural reasons for that: new companies are often founded by execs who think they can do better than the big companies they leave, infrastructure gets built up that benefits all in that given industry, talent begins to congregate in those areas, etc.
I think that different types of startups might be congregated around different geographic locales: biomedical startups would likely flourish near big research hospitals, etc. Service industry startups likely aren't clustered: restaurants, etc.
With technology startups, yes there is a natural clustering in Silicon Valley and Boston, but I think that's because tech startups are fairly new. I hear lots of good things coming out of Chicago, Austin, Columbus, Minneapolis, and elsewhere. It's definitely spreading.