Well, this is my theory after watching the entire season, reading that article and seeing some stats thrown in by fellow .netters:
We were league average or a bit worse on 3rd down %, and 3 and outs. Our passing offense was towards the bottom of the league in terms of attemps and yards. Our run game was, what...3rd ?
From watching the games, it was evident to me that when our rushing offense struggled, our entire offense struggled as is shown by the stats. Some folks were complaining that our route trees for WRs are extremely simple and easy to figure out due to our passing game being predicated off of play action and a strong run game.
My theory is that much of our offensive efficiency is due to having an elite defense that led the league in turnovers, thus putting our offense in a lot of favorable situations where they could score easily, without a lot of plays run. Honestly, I'd also theorize/speculate (I haven't done the research) that if you took out the points where the defense basically handed them to the offense with great field position, we'd be a league average offense (I'd speculate the same thing about SF).
Conclusion: There's a lot of talk about it being a passing league, then people use statistics to prove that running teams can win a lot of games and make deep playoff runs. Thing is, when teams stuffed our run and then blitzed us (not giving us time for routes to develop) it gave us a hell of a time and we generally didn't fare well. When we kept SF from beating us on the ground with Gore and Kaepernick, honestly not a one of us was worried that they'd beat us through the air.
So, SF goes out and gets Stevie Johnson and makes a concerted effort to shore up their WR corps.
What this tells us is that to be truly dominating, we need to have a balanced offense. Not necessarily pass more, but be better at it. That's why I think Harvin being back, and us drafting Norwood (yes, I think he makes the team, and makes a noticeable impact this season) is going to do a ton for our offense. If we can sustain more drives, we'll be more efficient and also control the clock a bit better. If teams stuff the run, we have to be able to gut out the tough passes and pick up difficult 3rd downs more often.