Flag does not equal bad. I think that’s where some of the concern lies. Flag is “hey, I need to get staff attention” for something. What’s something, well it might be bad, or it could simply be that a user needs staff for some reason. On one of the sites I moderate, we get flags for things like “hey, could you move this topic here”, or “hey, think you might like to see this”.
To use a real life example, my family once went to a giant corn maze. This was a maze so big that there were staff sitting in a watchtower in the center of the maze to keep an eye on things. All parties entering the maze were given a flag on a large stick, otherwise they had no way of communicating with the tower. The flag would be raised up and waved to get the towers attention for any reason. Most of the time the flag was used for “we give up, help us out please”, but it could also be used for something more important, like “I’ve found someone who fainted from the heat, send help!”.