Leaving aside the "noob" debate, the original post's preimse is whack. The 2006 defense gave up a ton of yards (both passing and rushing) in exactly one game - OSU, which, as noted, had the Heisman trophy winner. Then, against USC, unlike what the OP said ("My point is, the D has been susceptible to passing AND running attacks since the end of the 2006 season.") the game was 3-3 at half. As OP noted, USC couldn't run the ball for sh*t. Then, Carroll said, "Screw it" and just threw the ball.
USC had 48 total rushing yards (for a robust 2.1 YPC). So, no, the D's problems didn't start at the end of 2006. That was a great rushing defense and a pretty good pass defense. This year we have a below average rushing defense and an epically poor passing defense. Comparing them is not really comparable.