Because a Democrat is in the White House, would be my guess. NY Times Editor Bill Keller pretty much confirms it, saying that Democrats are nicer to the Times than Republicans (emphasis added):
Back in 2006 the conversations were professional and civil, but in the end when we didn’t agree to hold the story as they wanted us to, it was a kind of firestorm of criticism from the White House aimed at the Times. So far anyway we haven’t had that acrimony with this administration, nor as far as I know have other news organizations.
