He was booed because of the way he treated Rovers fans after he left.  At St James Park, the first game after he left us, we all gave a loud chorus of Shearer, Shearer before the game.  He kept his back resolutely to us for the entire time.  Contrast that with Henning Berg at Manure, who when we sang his name, came OVER to us and clapped. 
The man had no grace or class, therefore deserved what he got.  He also got an ovation as he went off after his 300th goal, and, I believe, didn't acknowledge the Rovers fans.