http://mmajunkie.com/news/14212/dana-white-on-officiating-gaffes-at-ufc-96-referees-need-to-be-confident.mma
The thing about Big John, and most "good" refs I think is that even if they stop a fight that could be considered early, they do it in a fashion where people feel like they made the right decision. I guess its that whole do it with confidence thing.
Dana's also criticized refs for stopping fights too soon, so his "confidence" critique is a bit hypocritical. Refs make mistakes but between UFC 95 and 96 we've seen a real drop in quality. Back in the day the only refs they'd have would be Big John, Herb Dean, Steve Mazzagatti, Mario Yamasaki, and Yves Lavigne. I don't know why they don't just stick with that crew.