I don't disagree with the Brady recommendation, necessarily, but I can see why some would pick Flacco. San Diego was absolutely terrible against the pass last year, and despite a lot of hype about an improved defensive scheme in the first full year under a new defensive coordinator, they showed the exact same weaknesses against Oakland: inability to pressure the QB, blown coverage on long passes, and confusion in the middle.
Add in the fact that Cam Cameron knows a thing or two about the Bolts D, and suddenly it's an interesting question.