1. Geography: Atlanta is sprawled out, so even if you live near Tech or Emory, odds are you can't skip down to the local coffee shop to get a feel what other startups are doing.
2. The Business Mix: Silicon Valley is tilted heavily toward technology in general and therefore also to startups (at least the kind we're talking about here). In Atlanta your friends and neighbors are likely to be bankers, accountants, healthcare professionals, or any number of corporate types than startup founders or even early-to-medium stage technology employees.
3. The Business Culture: There's little "porosity" among companies -- the knowledge/social network isn't there, and that's probably the most important ingredient of a startup hub, more important than money, IMO.
Interestingly, I think this might be an scenario where a YC clone could do the most good -- because as we are always hearing here, its real value is as an aggregator of like-minded people, enabling some of the knowledge interchange and social connections that don't happen naturally.