From a recent Wall Street Journal report:
Pakistan's leaders have publicly denounced U.S. missile strikes as an attack on the country's sovereignty, but privately Pakistani military and intelligence officers are aiding these attacks and have given significant support to recent U.S. missions, say officials from both countries.
American unmanned Predator aircraft have killed scores of Islamic militants in Pakistan in more than 30 missile strikes since August, provoking outrage in the South Asian nation.
As the report points out in no uncertain terms:
Yet, with the Taliban pushing deeper into the country, Pakistan's civilian and military leaders, while publicly condemning the attacks, have come to see the strikes as effective and are passing on intelligence that has helped recent missions, say officials from both countries.
The Pakistani military is apparently still trying to maintain its policy of plausible deniability:
Maj. Gen Akhtar Abbas, a spokesman for the military, said Pakistan and the U.S. "have a long history of military cooperation and intelligence sharing." But he said it doesn't include the missiles strikes. "We have made our opposition clear," he said. "The strikes are counterproductive."
But as the WSJ report goes on:
Other Pakistani] officials say President Asif Ali Zardari and top military leaders decided in recent months to aid the American effort in the hopes it will help them regain control over the tribal areas. The Taliban and al Qaeda have flourished in those areas bordering Afghanistan since 2001. The cooperation also could prove as a counterbalance to U.S. displeasure over a peace deal announced Monday with a Taliban faction in Swat Valley.
The protests are "really for the sake of public opinion," said one Pakistani official. "These operations are helping both sides. We are partners on this."
A former U.S. intelligence official said cooperation has always been strong between the two countries' intelligence services. "There's always been a double game," the former official said. "There's the game they'll play out in public [but] there has always been good cooperation."
Further evidence of the close working relationship between the two countries came last week, when Sen. Dianne Feinstein, a California Democrat who is chairwoman of the Senate Intelligence Committee, said the Predators are flown out of a base in Pakistan, not U.S. bases in Afghanistan, as many counterterrorism analysts had believed.
...Pakistan has since denied Ms. Feinstein's account, but former U.S. intelligence officials confirmed that it was accurate, lamenting the fact she stated it publicly. "It was a big mistake on her part," said one.