"Napster could have been used for legal means as well, and it got destroyed in court."
But Napster was a service run by an organization.
youtube-dl is neither a service nor an organization. It's just some source code floating around the internet, to which volunteers contribute to.
A very different situation.
If anything, it's Youtube itself that's like Napster, and it's telling that the RIAA has gone after youtube-dl rather than Google.