The only problem I see with reputation is that the users that post the most have the highest reputation. Negative reputation was removed a while ago, any downvotes you got before don't count.
Guys he's speaking figuratively. He means some people may be regarded as annoying, so their actual social reputation may be low. Not the website reputation. He says if someone is bad on the forums it is unfair for them to have a good reputation. As measured by the computer.