When Bush made the decision to invade Afghanistan he should have been prepared to face just the situation that Applebaum described. Yet his plan for Afghanistan has been almost exactly the opposite of what one would expect in such a situation.
He merely destroyed the central government and replaced it with a very lose confederation of tribes and regions. This obviously would lead to the exact results we now see. She then says that the small islands of calm created in Afghanistan show that hasn't been neglected. But if the intention was to end Afghanistan as a terrorist breading ground, the only possible measure of success would be the monopoly of military force held by central government. This was never attempted and so the goal of fighting terrorism in Afghanistan has never even begun.