The first state secrets case, dating to 1953, was used to cover up negligence, the New York Times points out in arguing that the Obamites have been over-using the doctrine, making many wonder whether crimes and negligence are being hidden.
The latest case involves a terrorist with U.S. citizenship who is on the government's death list as a legitimate target in time of war. Personally, I see the point of Obama issuing a death fatwa against this fellow. He issued a death fatwa against Molly Norris, the Seattle cartoonist who came up with "Everybody Draw Mohammed Day" in response to censorship of a South Park episode. The terror threats forced her to change her name and assume a new identity, thus effectively censoring an American who was excersising a fundamental American freedom.
Even so, the Times is correct to assert that overuse of the privilege invites bureaucrats and politicians to cover their butts with BS secrecy claims.