We've written a lot about protagonists over the years at the Blood-Red Pencil. Here is a selection of oldies-but-goodies:
Maryann Miller : Ask The Editor - How bad can a character be?
Kathryn Craft : Busted!—Janet Fitch caught championing an unlikable protagonist
Patricia Stoltey : One Method of Creating Characters in Fiction
Dani Greer : Hearing Voices: The Sound of Kindness
Shon Bacon : Building Character
Helen Ginger : Putting Yourself into Your Book