I really like the reputation system because I've been able to show certain people that I appreciate their help, contributions, them as an overall person, etc. and someone has made my day with one of the reasons they gave me reputation. Although this can also be done over PM system, I like this way better in showing your appreciation for someone.
As for negative reputation, that's something that you just have to figure out on your own. When the time comes to give someone negative reputation, I'm sure you will be able to notice it. If not, just avoid giving it and resort to just PMing the person with your disagreement, if it offended you, etc.
It's just that some people have to come along and ruin it. I honestly wish that some of us were a little more mature so that we can be able to handle things like this.