Ideally, the Cover 2 is the perfect defense. The reason why most teams don't run it or can't run it is because you need 4 lineman that are capable of creating pressure. That's a tall order these days but when your front four can pass rush, it can create havoc and lead to turnovers. The problem occurs when your front 4 can't rush the passer, then your secondary is basically playing a soft zone that is ripe for the picking. Indy has a great offensive line and thus Chicago's front 4 had difficulty generating pressure. When your front 4 is applying pressure, the QB is left to get rid of the ball quickly. And that's difficult to do against one corner playing up and a safety that his back which eliminates the deep throw. So a QB under pressure will have to be able to throw the perfect medium throw just over the corner and just short of the safety. That's nearly impossible to throw when a QB is under pressure. Very few QB's are even capable of making that type of throw.
Again, the reason we had trouble running it is because none of our lineman could pass rush.