As a I look across the league it appears that passing stats are down across the board. Granted 2011 was a historical season for QBs but I don't think anyone really thought that would trend down yet that is exactly what is happening this season. TD's are trending down, YDs are trending down and Y/A are trending way down. Perhaps it is unfair to expect Brady to even match last seasons #s when there appears to be a league wide adjustment favoring defense this season.
It's probably worth keeping in mind (both here and in the Cam Newton thread, for example) that these comparisons aren't just due to 2011 being "a historical season for QBs", but are also inflated due to 2011 being a historical season for lack of defensive preseason preparation due to the lockout. The QBs could be performing at precisely the same level that they were last season, but now opposing defenses are actually prepared for week 1 this time. That fact that this apparently makes no difference for the Patriots secondary does not mean that this is true for the league as a whole.