President Obama, who, as far as we know, had no direct knowledge of the investigations, has stated that he values freedom of the press, but also the need for the State Department to carry out covert missions, and to retain their secrets. In reality, that balance has tipped weightily in the direction of state secrets: the Obama Administration has launched more than twice the number of investigations into leaks as all other presidents combined. The case of James Rosen offers an example of a particularly deep investigation, though it is unclear just how many similar investigations there have been.
Rosen first caught the Obama Administration's eye when he released a story about North Korea's plans for more nuclear tests on the same day that a top secret briefing among high-level state department officials contained the same intelligence. Soon after, the FBI was on the case, and flagged Kim as the likely source. The Washington Post reported that FBI Agent Reginald Reyes compiled a case using security-badge data, phone records and emails linking Kim to Rosen:
“Mr. Kim departed DoS [the State Department office] at or around 12:02 p.m. followed shortly thereafter by the reporter at or around 12:03 p.m.,” Reyes wrote. Next, the agent said, “Mr. Kim returned to DoS at or around 12:26 p.m. followed shortly thereafter by the reporter at or around 12:30 p.m.”
The activity, Reyes wrote in an affidavit, suggested a “face-to-face” meeting between the two men. “Within a few hours after those nearly simultaneous exits and entries at DoS, the June 2009 article was published on the Internet,” he wrote.
On one hand, the State Department has enough to worry about without reporters leaking their secrets, on the other hand, it's a slippery slope from state secrets that endanger innocent lives if shared to inconvenient truths that the government would prefer not to share. That's why these disputes are supposed to be decided by a judge, but the Obama Administration chose not to work through the judicial system, and instead took matters into their own hands. Republicans are solidly on the pro-State Department side of this, so the scandal likely won't get the same attention as the IRS scandal, but objectively it's a bigger deal, and a harder nut to crack. Generally, however, humanity has done better when it leans to the side of the free press.