Berman is the captain of the ship. He may take orders from a higher source, but it his captaincy that sets the tone for the ship. Under his command, the ship foundered.
And he went down with the ship.
From what it sounded like in an interview, Paramount went ahead with Star Trek 2009 without letting him know Trek was no longer his. What was going on with him between 2005 and 2007?