Consider this: The top 5 QB ratings in the league are Rodgers, Brady, Brees, Romo, and Schaub.
After that, it's Manning, Roethlisberger, Smith, Stafford, and MATT MOORE rounding out the top ten.
If that doesn't convince you that a QB Rating is an imperfect way of measuring QB performance, I'm not sure what will. Very few people here would argue that Romo, Schaub, Smith, or Moore are better than Flacco. That's a pretty untenable position.
One might be able to argue that Roethlisberger, Manning, or Stafford are better. (One could argue Schaub statistically but Flacco is 2-0 against him now.) Stafford has scored a ton of points, and Ben and Eli have their rings. I personally wouldn't make those arguments, but you're not getting laughed out of the room if you do.
I haven't even mentioned Phillip Rivers since his team is awful and his performance has been awful. I'm not at all sure what is happening with him right now, but it's hard to call him "elite."
So where does that put Flacco? He's certainly not as good as Rodgers, Brady, or Brees. He's squarely in that league of Ben, Eli, Stafford, and Schaub (with a clear edge on Schaub and Stafford, in my mind). Flacco, by that metric, is at least the 6th best QB in the NFL.
4) Roethlisberger (cringing)
9-32) Everyone else...
If Flacco isn't elite, he's damn close.