At Bayern, Klinsmann had dressing room problems. He loved to talk about scientific methods and a new approach based on using technology (sound familiar?) but players complained to the papers that he knew nothing about tactics, and he was all about giving empty motivational speeches.
His bringing in Vasquez and Donovan were viewed as bad moves that showed how disconnected he'd become in California. Keep an eye on Vasquez in the TFC process now.
He wasn't popular with the Bayern fans - they didn't like that he quit Deutschland after 2006, he wasn't really a "Bayern guy" (he spent most of his best years elsewhere), he didn't move to Munich (this "affront" generated a lot of press), and he's got an aloof style that didn't work well with the media.