Comments serve an auxiliary function; they exist to support the all-important questions and answers. The goal is not to generate more comments, but better Q&A.
As such, you should assume that comments will be temporary; if you're putting information into a comment that would be nice to have around long-term, consider trying to work it into the question or an answer instead.
Granting reputation for comment votes would create a perverse incentive to post more of them and keep them around longer, potentially resulting in situations where questions and answers are buried under scores of kibitzing comments - the sorry state so many forums find themselves in.
Also, we'd probably have to implement downvotes.