The reputation system is not a measure of ONE reply. It is a measure of the replier. For example, there are people on here that contributed quite a bit in replies. Some may be helpful, some may not be, although all replies are beneficial. The reputation system allows you to help "grade" the person and over time it will show who is providing more quality replies.
So again, the system is NOT on a per thread/per post basis, but a measure of the actual person and their contributions.