I doubt it has anything to do with the South. Vermont is a state that favors small businesses (the only large employer I can think of is IBM in Burlington; I assume that Ben&Jerry is also a large employer but they're a local company). Places where small businesses can flourish seem to be more liberal because they have more of a personality (as opposed to places where everyone shops at Walmart and eats at MacDonalds).
It's also a very liberal place culturally, with artist-colonies and many neo-hippies, who enjoy their weed in public. It's also quite secular and I think proximity to Quebec has played a role in their acceptance of different cultures (you can for example listen to Quebec radio stations in Vermont).
I don't think Vermont is as liberal as many believe it is, but I guess in national elections people realize how far to the right the GOP is.
I would have thought small business owners would be more likely to support the GOP as generally excessive regulation and high taxes hurts them more due to low profit, although I do see the lack of some multinationals may be more a reflection of the liberal attitude rather than what creates it. The Quebec proximity is an interesting one, certainly in New York the areas near the Quebec border are more Democrat, but you don't see that in New Hampshire or Maine, in fact in Maine the areas near the Quebec border are more competitive then areas further south. Likewise Democrat support is pretty solid even in the southern sections.
It is odd though that Vermont is the whitest state and Obama's second best if you exclude DC which is kind of ironic as white voters are who he did worst amongst. And the fact it votes GOP at state or local levels albeit more moderate ones is also a sign of the GOP's rightward drift nationally hurting them here.
