Agree that this is the issue but I don't agree that the scheme is to blame. To me it is obviously the talent. Safeties and ILB are most commonly responsible for the middle of the field and since our superbowl I'm doubting there are any other contenders out there who've had less at those positions than us.
Even before the superbowl we had some seriously athletically challenged dudes in Bishop, Hawk + 20lbs, and Peprah but with Woodson perpetually in the slot and Nick Collins taking away the seam, teams had a major deterrent from spamming the middle of the field. With those two gone and the better athletes like Jones and McMillian not working out we were hosed.
The other thing to blame is league trend. The middle of the field is hot right now. I heard a stat somewhere that something like 70% of the passes in the NFL were in the middle of the field last year. So its something every defense is having to deal with but we've been uniquely vulnerable there. I'm optimistic about it just because we've got some new blood in there and our safeties are playing well.