What we often forget these days is that it wasn't always that way. New England was originally settled by Puritan "theocrats" when the South was populated by loose-living Anglicans. It was America's original Bible Belt and the home of America's first "red scare" in the days of the French Revolution. Rev. Timothy Dwight of Yale University (though it was probably still just Yale College then) put out a pamphlet attacking Voltaire and the Bavarian Illuminati. Plus New England Federalists (America's original conservatives) thought the South's slave-owning aristocrats were a bunch of Jacobins and that Thomas Jefferson was going to confiscate all the Bibles in the country.
Unfortunately the very children and grandchildren of the conservative Federalists were already becoming radicalized into (radical) abolitionism, Transcendentalism, women's rights, and such like. And ironically, the bridge from Federalism to radicalism were temperance, anti-Catholicism, and anti-Masonry--things now associated with the conservative Bible Belt.
Even after the spate of mid nineteenth century Yankee radicalism, New England was often seen as the ultimate down-home America. Its mystique inspired the creation of such characters as "Uncle Josh" and Longfellow Deeds.
I must confess to having a love affair with old, traditional New England (especially the now extinct Yankee accent best known through Parker Fennelley's radio character "Titus Moody"). It's really infuriating to me that NE has come to represent what it now does. The sort of thing happened to the Jews whose stereotype somehow went from Canaanite-killing religious fanatics to dirty stand-up comics.