"Because so many sites — including TIME — use Facebook's user-tracking "Like" button, Zuckerberg is able to collect information about people who aren't even users of his site. These are precedents which hurt our ability to freely connect with each other"
Nope - it just hurts our ability to connect privately. Not the same thing.
"The fact that Facebook's code is hidden from view means that its users are not connecting directly with each other. They are speaking to Mr. Zuckerberg [...]"
What does Facebook being open-source or not have anything to do with it? Does Word being closed-source mean that everything I write in Word is really a communication to Microsoft?
Even worse, that sentence leads to this:
"witness the recent reports of Facebook's messaging service blocking messages based on the words and links in them, because those links point to services which Facebook would prefer we not discuss."
I'm assuming this is about Facebook blocking links to Lamebook. According to Tech Crunch, this went on for only a few hours. It was probably a bug/mistake - I can imagine the same thing happening from Gmail or any other mail provider. TC article: http://techcrunch.com/2010/11/22/facebook-censorship/