Megaupload wasn’t even hiding behind a legitimate use case. It couldn’t be used as a personal file storage service because infrequently downloaded files would be deleted. The company paid people to upload popular files. The service had a comprehensive CSAM takedown process but no such process for copyright infringement.
Basically, the US government was saying that Megaupload’s intent was extremely obvious.
Sites like Crunchyroll and YouTube which started off being a haven for piracy had DCMA compliance as their shield. They complied with requests to take down content and weren’t building the entire business around infringement.
Plex doesn’t enable you to distribute content beyond your household, and it’s also facilitating legal personal backups of commercial content.
Google Play Music (and iTunes for that matter) were the same thing: making backups of your music is completely legal. Google Play wasn’t telling you to jump on LimeWire to illegally download your music.