On surface settlements, NPCs tend to be grouchy and very rude to cmdrs—particularly security officers. If I go into a bar at a tourist settlement, the staff and patrons should be like “welcome, take a load off Cmdr,” instead they’re like “what are you doing? You’re too close. why are you here? I’m sure you’re here for something…”
When a Cmdr has good rep with a faction the NPCs should be friendly and welcoming IMO.
Put yourself in their shoes for a second.
You're doing your job, policing some boring settlement somewhere. Once in a while there's a person from infamous Pilot's Federation visiting. They're easy to recognize, because almost every one of them is running around like a crazy person, opening every possible door, looking into containers, downloading your emails and stealing ebooks.
And when you ask him politely to stop and submit to a scan, they don't pay any attention to you and sometimes even reach for their gun.
So you shoot them.
And then all hell breaks loose. There's whining on some forums somewhere, people call you a "kill-joy" and want you to get "nerfed".
Would you be nice to another one you see? I don't think so.