Might it be that some of the users' shared content on Megaupload was copyright protected? Absolutely. It is nearly impossible not to violate the law, as shown by SOPA sponsor Lamar Smith's own campaign website, which used an unattributed background image in technical violation of the law. The leading opponent of piracy might himself be a pirate!
I have not read every in and out on the debate on intellectual property but bit by bit I'm coming closer to the idea that there shouldn't be any or that, at least, there should be much less protection of it than there is now. One thing that informs my view is what I learned from Sam Peltzman in my Industrial Organization class at UCLA in the early 1970s. When we got to patents, I thought we would hear the standard case for monopoly as a spur to innovation. Sam did present that case but he also put on the syllabus two articles by Arnold Plant from the 1930s that expressed skepticism about IP: one was on patents and one was on copyrights.
My Encyclopedia (first and second editions) covers both. For a full-throated defense of IP, see Stan Liebowitz, "Intellectual Property." In the earlier edition, I wrote the article on patents and pointed out the difficulty that Arnold Plant had noted. See David R. Henderson, "Patents."