i don't really think it's much of a secret that megaupload was widely used for piracy... why is it surprising?
Because tons of alternatives exist that weren't taken down, and normally the DMCA safe harbor clause would shield them from this sort of thing.
This strikes me as a bit of an easy thing to say, that it's common sense that something like this would happen because "everybody knows" it's used only for piracy.
I mean, what are they gonna take down next? Mediafire? Rapidshare? Dropbox? Youtube? Legally there's no difference depending on how pervasive piracy is on a particular website, and there's a very specific protocol that has to be followed. If a website responds to takedown claims as outlined by the DMCA (which is extremely slanted to favor the copyright business) it should shield them from scrutiny.
Although I haven't really followed it that closely it seems they might have been involved in money laundering as well, so that might be the reason why they were targeted in particular. At the very least it puts into question the idea of them being taken down because they were actively and knowingly aiding copyright infringement.
Also apparently one of the people who was arrested has the last name Dotcom.