Usually, when the phrase small-town charm is used, there is an implication that the charm comes from the relaxed, genuine or unpretentious characteristic of small towns, as well as the fact that small towns can be cute or quirky in a way that big cities can't.
This tourism website encouraging people to visit small towns in Minnesota, and this article describing various charming features of a small town in Ohio, provide illustrative examples of how small-town charm is used.
Due to the characteristics of small towns I listed above, the phrase could also evoke connotations of being uneducated, which the writer in your excerpt is specifically contradicting. You could paraphrase the excerpt something like this:
Despite the light / casual / unpretentious nature of his writing, Tim is undoubtedly an expert.