I'm not 100% sure I buy that Shanny didn't win 'because of the organization' - the dysfunction certainly didn't help but I think he had a hand in a lot of the drama himself.
Here's how I see it. Coaches are human beings. Once you've climbed a mountain and been to the top, the motivation to do everything it takes to get there again is usually diminished. It's simply human nature. Achieving a huge goal, one naturally loses some of the drive, intensity, and motivation to achieve it again.
The other aspect is, it's incredibly difficult to get to a Super Bowl, and to win one - much less return repeatedly. So many things have to go right and work. Not only do you have to assemble a team of coaches that mesh, get the best out of their players, and keep them from continually getting poached by other teams, you have to obtain/grow the talent on your roster, and have systems that take advantage of their unique talents. Do all those things well and you may consistently get to the playoffs. Then you have to hope that you don't experience any crippling injuries, outcoach other outstanding coaches every game enroute, and hope you aren't the victim of horrible game-turning officiating calls. And on top of all that - you have to have some luck.
Look at Joe Gibbs in his 2nd gig. Does anyone really believe Joe wasn't the same football genius and master motivator in round 2 that he was in round 1? He was exactly the same guy. But he lacked many of the things required to truly succeed. A great front office, players that fit what he was trying to do and had the talent to get it done. Even luck conspired against him as we had some brutally bad luck in his playoff appearances.
Taking two or more franchises all the way to Super Bowls is an incredibly rare accomplishment for an NFL head coach - because it's an incredibly hard challenge.