Independent pirates who don't work for anyone but themselves are in every aspect an annoyance to the Rogues. They're nothing more but competitors who don't wish to work together with them, or be of any use for them at all. They use their piracy grounds, shoot/hunt them (over 50% of them in reality), and do use the Rogues' bases "for free".
While I must admit that I support the vanilla pirate groups like Lane Hackers (of which you rarely see indies), and dislike the terrorist-like Pirate ID which can be (ab)used by anyone. And it's sad to say, but there are only a few who actually RP with the Rogues, giving them a reason to have them docking on their bases.
Like it's often the case, the well-doing other half has to suffer of such changes. So they either have to use Rogue/Hacker/Junker/Freelancer IDs now.