I don't think the FBI shut them down.. Didn't they do it themselves as a precaution?
No.
Kim Dotcom resides in New Zealand so I've seen the developments of the story constantly.
The FBI shut it down and seized servers. Police also raided Dotcom's mansion and seized millions of dollars, vehicles, and have prevented him leaving the country, etc.
Fortunately the New Zealand court system isn't going to bend over to the US like certain other handicapped governments might want to, so Dotcom seems to be the one with the upper hand as courts are rejecting the American FBI's actions as being lawful, etc. He appears to be getting seized assets back bit by bit and is building a defense case.
I personally don't believe a file hosting website can be held accountable for material people upload. Ridiculous.