Steve Coll argues (convincingly) that the Justice Departments disclosed surveillance of the press is only the tip of the iceberg, and originates somewhere deeper than presidential disposition:

It seems likely that Holder or his deputies have authorized other press subpoenas and surveillance regimes that have not yet been disclosed. The Justice Department has acted belligerently even in cases where no grave harm to the public interest has been demonstrated, or where, as in the A.P. case, the leaks under suspicion have served to publicize the Administration's successes. Why would the President preside over such illiberal decisions? His longest-serving advisers are disciplined and insular to a fault; press leaks offend their aesthetic of power. And it would hardly be surprising if Obama viscerally disdained the media's self-important excesses. Yet the Administration's record cannot be chalked up to the President's temperament or to Holder's poor judgment alone. 

It is no coincidence that the A.P. and the Fox cases arose from national-security reporting. Obama inherited a bloated national-security state. It contains far too many official secrets and far too many secret-keepers -- more than a million people now hold top-secret clearances. Under a thirty-year-old executive order issued by the White House, the intelligence agencies must inform the Justice Department whenever they believe that classified information has been disclosed illegally to the press. These referrals operate on a kind of automatic pilot, and the system is unbalanced. Prosecutors in Justice's national-security division initially decide on whether to make a criminal case or to defer to the First Amendment. The record shows that in recent years the division has been bent on action. 

Last month, at the National Defense University, Obama pledged to end America's formal war on terrorist groups. His speech was one of the most impressive of his second term. He announced renewed plans to close Guantánamo, and he promised to tighten the rules governing classified drone strikes. He made no mention, though, of the many examples of investigative reporting -- about the torture and abuse of prisoners, about official lies issued by the Bush Administration on the road to war in Iraq, about targeting errors in drone attacks -- that have helped to discredit the policies he now seeks to wind down.
I think that last point is really key. Many of the debates we are having, and have had, would be impossible without leaks. (Chris Hayes details them a few of them above.) It's perhaps a self-serving cliché to point out the need for an oppositional press in an actual democracy. But it's also a fact. Not to take away from Coll's point, but I think this (typically) excellent Jane Mayer piece on how the president handles whistle-blowers is worth a re-read.