Check this and
this and
this.
This will help heaps, there was a pretty heated disucssion on Reputation points.
To answer your question, if you feel you have been given a negative reputation point unfairly, then just let Brandon know pointing out to the post. If it is really unfair, he will look into it, if my memory serves me right.
The
FAQ system explains very well the use of Reputation system. Ofcourse its not flawless, but it does serve its purpose. I use the reputation system extensively, and from what I do, I can say, give reputation points for good posts, and negative points for pointless posts(exclude chit-chat). Read the FAQ, it explains well. Also, the thread about Reputation System, I am pretty sure it will help you.
If you still have questions, I am sure one of the moderators or Brandon will be happy to answer your question.
-Bharat