Here is a different take on the subject tptacek.
It is unlikely that NYT is ordered to produce stories according to the current administration's liking. Broadly in the West we don't go in for that sort of thing and one hopes we never will.
We don't like being told what to think. The trouble though, is that all ideas have to come from somewhere.
The power of Western style propaganda is that the government does not have to orchestrate it as intensely as in autocracies. It happens automatically because they live and breathe the same air. The relationship is more symbiotic.
If you have real power, you can afford not to be petty. That is the same deal as with the Joker in the medieval court with the King. A government official only kills journalists were they a real threat to his power. If you punish people for a small degree of insolence it is because you are not secure in your power and any provocation could be used to coordinate an attack to displace you. Being 'above' that is a tacit demonstration of power and stability (a good thing!).
What is the practical difference between the information printed by the New York Times and the opinions of the State Department?
I cannot think of any. Any divisions I see are also expressed within the government itself. So they must be coordinated. But is it really from government to media?
The neo-reactionary take is basically the exact reverse of this:
"The New York Times is not in fact an instrument of the US Government."
That's not as whack-a-doodle as it at first sounds. The New York Times is the mouth of a much larger network they refer to as the Cathedral, just as Christianity is not just the physical Vatican City.
This is not necessarily an 'evil' to vanquish, but it does mean if the NYT is misguided on some subject, then it invariably also means the government too is running into the same dead end.
The long and short of it is that the press and the government sup from the same pool of propaganda while they generate it, they believe in their own manufactures. I hope this makes sense to you.