Edit: Leaving the original text so as not to confuse the conversation. Megaupload is a foreign (to the US) site with a US TLD, not a US-domestic site. The arrests were made around the globe, but mostly in New Zealand. The FBI may have initiated the indictment, but extradition applies, as does the Berne Convention.

SOPA and PIPA are intended to address issues with foreign-hosted sites being used by Americans to pirate American copyrighted works. MegaUpload is a domestic outfit, so they fall under existing copyright law, including DMCA.

The issue with fighting foreign-based sites is that they don't fall under US jurisdiction. Up till now, the RIAA and MPAA have taken to suing Americans using those services. However, that's not really putting a dent in piracy. So, they came up with SOPA and PIPA. Of course, how do you stop Americans from visiting foreign sites which you have no jurisdiction over? Using DNS filtering is the answer they came up with. Of course, they left the language fairly broad, and now they've stricken that part from the bill.

The real issue with SOPA and PIPA is the removal of due process. Since the laws deal with foreign entities, though, the waters get muddied.