Indeed your quick analysis is true: MegaUpload was a platform to download copyrighted things over the internet.
But there is a greater principle at play: when should action be taken? The way it is done in democracy and countries where liberty is valued is that the action taken is done after due process. Also and I think this is pretty damn important there are international rules in terms of law and what can be done. Citizens of other countries should have the right to benefit from the law in vigor in their country without the US interfering with them. The US is not all saint and sometimes take poor decisions that cost the business, health or life of some people, especially when the problem comes from private interests.
Anyway if you allow authorities to take action without due process you end up in dark dark world where arrests become arbitrary. There were plenty of evidence that MegaUpload business was not legit actions could have been taken legally, but probably bribes came into play and short-circuited the whole thing. This becomes rampant in the US (Bradley Manning anyone ?) and it has to stop before it's too late.