This has baffled many, who is really in charge of Pakistan?
The general perception is Gen Kayani, and the civil government is just a puppet in the army hands.
It is well known that the foreign policy, the defence and finance is controlled by the army.
Also I think Pakistan can object only when it believes innocents have been killed in Drone attacks. So far the attacks have been pin point accurate and all those killed are millitants, as has been reported Daily in the Pakistan news papers... that so many millitants killed in drone attack etc etc. So the USA is in reality making Pakistan armys job easier.