It's a point of view thing. Mal and the others weren't the good heroes we expect them to be. It's the whole glorification of the drifter/tough guy/Han Solo-esque characters that pop up from time to time. The Alliance weren't necessarily good or bad, but they were the WINNERS of the war, which polarises the characters and sets them off as they do.
Unfortunately Whedon (like the Trek Movies) does like to portray authority figures as slightly less intelligent or informed as the main characters (for example the Reaver situation in Bushwhacked