We do make the appropriate changes to remove the unwarranted bad reputation and we do also ask for explanations from the bad rep trigger happy fellow.
If you think that someone abused the reputation system and gave you bad reputation points for "no good reason", then just tell us.
And remember, unwarranted bad reputation is the one received for a neutral/correct post of yours.
If you receive bad reputation for a post where you showed a confrontational, or agressive, behavior, you deserve it.