According to this question, reputation is a "broad aggregate representation of the trust the community puts in you."
However, it seems to me that the more "popular" a platform is, the more likely your answer will get seen, and the more likely it is to be voted on.
Your "reputation" then, is a function of both the trust the community places in you, and the size of the community that is interested in the same thing.
It is entirely possible for someone with deep knowledge in domains that most programmers care less about to have significantly less reputation than someone who has modest knowledge of a more popular subject. Note especially that the questions that generate the most reputation seem to be generic opinion based queries. The kind that often generate flame wars because people are passionate about them.
I am not saying that such questions are necessarily bad, my point is just that reputation has a strong dependency on the number of people interested in looking at the question, and a much more tenuous connection to the actual competency of the answerer.