Actually they are struggling for several reasons:
1)Parity-There is true parity in the NFL
2)Sports is cyclical- Believe it or not, the Pats used to suck, and they will suck again some day (hopefully not for 10 years or so). Sports is cyclical, there was a time where the 49er's were pretty bad, Then they win 5 SB's in 15 years, and now they suck again (they may be making that turn around). That's how sports is, hell the Yankees went from 1978-1996 without a World Series championship.
3)Free agency-Look at the Colts, losing Edgerrin, a linebacker, and a defensive lineman, all important to their team. Same with the Pats, who no longer have their SB receivers (One FA and one trade) or kicker.
Those are just three reasons, I think 1 and 2 are key reasons.