PFF and other similar sites use a lot of subjective analysis. The stats you list are objective measures. It isn't a matter of PFF being unaware of the stats you mention, it is that they do not consider a TD pass, or any other objective stat, a standard unit of measurement with a constant value. This is also the case with the ESPN QBR stat (subjective analysis plays massive part in the stat, unlike traditional QB rating stat).

I don't see any real reason why these sites or experts would have a personal bias against Flacco, but I do agree that their subjective measures seem to penalize Flacco (and probably others) in some way, shape, or form. They tend to be more inclined to conclude that Flacco is taking what is given when he succeeds, and that Flacco is failing to take what is given when he fails; therefore they underweight his achievements (good games) and overweight his failures (bad games).