After explaining that Pakistan does what it must regarding Afghanistan to keep us as an ally to keep India contained and yet also caps their efforts to avoid a popular revolt, Stratfor addresses our angle:
The Americans were, of course, completely aware of the Pakistani limits and did not ultimately object to this arrangement. The United States did not want a coup in Islamabad, nor did it want massive civil unrest. The United States needed Pakistan on whatever terms the Pakistanis could provide help. It needed the supply line through Pakistan from Karachi to the Khyber Pass. And while it might not get complete intelligence from Pakistan, the intelligence it did get was invaluable. Moreover, while the Pakistanis could not close the Afghan Taliban sanctuaries in Pakistan, they could limit them and control their operation to some extent. The Americans were as aware as the Pakistanis that the choice was between full and limited cooperation, but could well be between limited and no cooperation, because the government might well not survive full cooperation. The Americans thus took what they could get.
Take what we can get. I'm a realist here. Do we really want to push Paksitan to do more than it can bear and risk losing Pakistan as an ally in the war? Do we want to risk Pakistan's nukes getting loose or--far worse--coming under the control of an Islamist regime?
We'll have more freedom of action once we win the war in Afghanistan to apply pressure on Pakistan to behave. Unfortunately, I'm sure Pakistan is well aware of that.