Nice article. I think it all comes down to the fact that this type of attack had never happened before. I am more inclined to believe that America was caught with its collective pants down and responded to slowly. History will show that most big social/political changes (in America and every country) are typically made immediately following a catastrophic or large scale, or first time event. governments are typically reactive and not proactive. So it takes an event like 9/11 to motivate massive changes that almost always follow an event like that.
So I would not go as far as saying that our government allowed it to happen as much as it did happen because of our inability to act fast enough, no prior experience with a similar situation, etc.