Megaupload has been shutdown as their is reasonable suspicion that it is encouraging the illegal distribution of copyrighted material. Whether or not those arrested are found guilty of such will, of course, be decided by a jury of their peers and a later date.
Prior to the trial, the site has been shutdown - this is perfectly in line with the legal situation in every country with a common law system (not just the USA), and I'd wager is the case in civil law countries - for one thing, a legal system cannot allow the continuation of potentially illegal activity following arrest. Secondly, one cannot be allowed to profit from a crime. To use an example, once someone has been arrested for illegally manufacturing narcotics, the drug factory would not be allowed to continue producing cocaine - even if the defendant claims that that white stuff is talcum powder.
I hasten to add that the lack of judicial overview and the lack of recourse or appeal are reasons why I was against SOPA/PIPA - but I'm not going to have a go at something that is merely treating piracy as no different from any other crime - as is the case here.
Now, that said, I do not think that such takedowns are a practical way of actually combating piracy - too expensive, the returns are too few, and frankly it'll never really solve the problem, and I feel that the industry's affected could make quite a number of changes to their business models and distribution that would both seriously undermine the pirates and be profitable for the producers. However, Megaupload managed to make the great mistake of getting itself an awful lot of publicity recently - once that happens, demands grow for action to be taken, and government agencies end up looking rather ineffective if action is not taken (a bit iffy, but understandable.) I appreciate that a lot of legitimate users have been screwed over due to the recent take-down (again, I re-iterate, I do not think such tactics are really a long term effective remedy), but the blame lays squarely at Megaupload for not being seen to do enough about the alleged illegal side of it's operations, being stupid enough to bloody advertise (which is frankly, retarded, when there is little argument that there was an illegal part of their operations), and getting itself in the news.
EDIT: as an addendum to the above, the takedown of Megaupload may actually HINDER the passing of future anti-piracy bills in the future. If the current law is seen to be working, then the impetus to introduce new ones will be severely reduced