This ought to have been apparent 20 years ago. Anybody else remember Judith Miller and her little pas de deux with Dick Cheney, where his office would "leak" phony intelligence about Iraq's WMD program to her, she'd publish it in her New York Times column, and then the Bushies could cite it as evidence? Pepperidge Farm also remembers the non-apology apology the editor published (buried well off the front page) that conspicuously missed anything about not letting the paper be used as a mouthpiece for the state in the future.
The only reason that it ever had a progressive reputation is because the GOP/Tea Party kept shrieking about "liberal media" to move the Overton Window to the far right.