I have a good friend -- he's been to our apartment and eaten our food and watched our movies. He's a genuinely nice guy and has a dress collection (for his character) almost as big as mine.
He hasn't led a lot of instances as far as I know, and he's not particularly gear-centric, though he works on his gear to be able to raid. He's a big supporter of the way our guild hands out loot, which is to spread it evenly among as many people as possible.
He led a 25-man Archavon, on master looter, and three rogue pieces dropped. He and several other rogues rolled, and one rogue rolled 100 on two pieces.
My husband suggested to our friend that he put the loot rules in writing at the start of the raid next time, because our friend handed the loot out as our guild would have -- one person can get a max of one loot per run unless uncontested, so he handed the loot to the second highest roll on the second piece of gear.
The problem was that the second highest roll was . . . himself.
So, essentially, the rogue that rolled both 100's saw him as ninjaing loot. Now, I know him better than that. He was doing what he saw as most fair, not most beneficial to himself. He would have done it for anyone. He just didn't expect anyone to roll highest twice in a row and thus didn't plan for the situation before it arose. And the other rogue continued his bashing of my friend in the raid, in whispers, and later in trade chat. And . . . this animosity honestly bothered my friend. I think he would go back and do things differently if it meant making it all go away, even though he was truly just trying to be fair.
When someone makes a faux pas (in this case, not saying one loot per person before the loot dropped), and people refuse to believe that it wasn't greed and ninjaing, how do you get your reputation back?
In my opinion, you ride the waves, hope people attribute the bitter "I love gear more than people" rogue to just another "didn't get what I want" whiner, and you work to preempt similar problems next time.
You can't rebuild a reputation by arguing, but you can rebuild it by showing people through your methods and actions that you are what you say you are.
Art of my friend's rogue by guildmate Velandrea.