User blog comment:12th Supernova/Chapter 793: Bad News and Bad Translations/@comment-4503935-20150709200130/@comment-24769684-20150710135654

Because he was the one who actually (though inadvertently) caused the chaos on Dressrosa! Luffy only cleaned things up. Plus, the World Government knows how powerful Doflamingo is, hence when they wrapped him in Seastone shackles, and anyone considered to be a great threat to Doflamingo is a great threat to the World Government.