You're right to be shocked about the NYT calling for the breakup of facebook, but I think your a bit off on the 'why'. I say you're right to be shocked because Facebook is run by a person who some on the left were previously calling to make a presidential run, who was previously a shining beacon to the world's left-dominated media (including the NYT) ... so yeah, it's kind of shocking to see how quickly they've turned on Zuckerberg and Facebook.
The real story of 'why' the about face has to do with Cambridge Analytica, though. Many in the media still feel that the election 'should' have gone the other way (regardless of how people actually voted), and now they blame FB/Zuck. The irony is that in 2008 Obama's team did all of the same things that Trump's did. The media was OK with it then (in fact, celebrated it) because it was for their side.