We study structural and topological properties of nested set complexes of matroids with arbitrary building sets, proving that these complexes are vertex decomposable and admit convex ear decompositions. These results unify and generalize several recent and classical theorems on Bergman complexes and augmented Bergman complexes of matroids. As a first application, we show that the $h$-vector of a nested set complex is strongly flawless and, in particular, top-heavy. We then specialize to the boundary complex of the Deligne--Mumford--Knudsen moduli space $\overline{\mathcal{M}}_{0, n}$ of rational stable marked curves, which coincides with the complex of trees, establishing new structural decomposition theorems and deriving combinatorial formulas for its face enumeration polynomials.