Howard Dean comes from outside of Washington. He's never been that close to Washington culture; he doesn't have a ton of contacts that owe him favors or go to all the cocktail parties there, and the Washington political and media elite don't consider Dean to be one of them. He goes home on the weekends and stays in a hotel while he's in DC. The Clintons don't particularly like Howard Dean, partly because they've never been close or worked in the same circles, partly because of significantly differing ideologies of how to manage a national party, and partly because Dean did something completely unexpected from a DNC chair when two big, swaggering, powerful swing states decided to flout the universally accepted party rules and cut to the front of the line: he put his foot down, and hasn't budged since. He doesn't even try to contact their party heads to stroke their egos or listen to their whining.
Curiously, Adam Nagourney and The NY Times think this is a bad thing.