I'm also a bit surprised to see Coop on the other side of this one from me, since I think a lot of the arguments for (and against) Rodgers are the same as the arguments for (and against) Gronkowski. Both provide a huge positional advantage. Both play at historically undervalued positions. Both guys suffer from the fact that you can only start 1 player at that particular position (although some leagues allow a 2nd TE to be flexed, realistically speaking, "flex-worthy" is a pretty high bar for most non-Gronk/Graham TEs to clear).
I always assume TE is a flex-eligible position, as it is in all of my leagues. I'd be a lot higher on Rodgers if it the gap between he and the #2 QB was as wide as Gronk/Graham and the field.
Top 12 PPG QBs in the HyperActive leagues last season:
1. Peyton - 30.6
2. Brees - 26.6
3. Foles - 22.7
4. Rodgers - 22.3
5. Dalton - 22.3
6. Stafford - 22.0
7. Rivers - 21.8
8. Newton - 21.7
9. Luck - 21.5
10. Romo - 20.7
11. Roethlisberger - 20.5
12. Griffin - 20.4
Pretty flat after the top two guys. It's a similar story at most of the other positions, but the key difference IMO is that you can stack up multiple great RB/WR whereas you can only start the one QB. If you have QB1 and QB5 on your roster, you're getting a big advantage at your QB1 spot but that QB5 isn't doing you any good because he's on your bench every week. If you have WR1 and WR5, you're getting a big advantage at your WR1 spot and also at your WR2 spot where that second elite WR is giving you a huge weekly edge.
Different formats require different approaches, but in leagues like these, I think it makes a lot of sense to basically disregard the QB position.
If you KNOW that your QB is going to score out of his mind like Peyton and Brees then that's one thing, but in general there's simply a much bigger edge to be gained by taking shots at WR/RB where you can utilize multiple great players to start to gain a really big weekly advantage. Last season Julian Edelman, TY Hilton, and DeSean Jackson probably did more to help you win in that format than Rodgers or Foles. Anything short of INSANE QB production just isn't that valuable.
In another league, it might be a different story. I'd say QB production is of minimal concern to me in 5/7 of my dynasty leagues though.