We study the automorphism groups of countable homogeneous directed graphs (and some additional homogeneous structures) from the point of view of topological dynamics. We determine precisely which of these automorphism groups are amenable (in their natural topologies). For those which are amenable, we determine whether they are uniquely ergodic, leaving unsettled precisely one case (the ‘semi-generic’ complete multipartite directed graph). We also consider the Hrushovski property. For most of our results we use the various techniques of Angel et al [Random orderings and unique ergodicity of automorphism groups. J. Eur. Math. Soc., 16 (2014), 2059–2095], suitably generalized to a context in which the universal minimal flow is not necessarily the space of all orders. Negative results concerning amenability rely on constructions of the type considered in Zucker [Amenability and unique ergodicity of automorphism groups of Fraïssé structures. Fund. Math., 226 (2014), 41–61]. An additional class of structures (compositions) may be handled directly on the basis of very general principles. The starting point in all cases is the determination of the universal minimal flow for the automorphism group, which in the context of countable homogeneous directed graphs is given in Jasiński et al [Ramsey precompact expansions of homogeneous directed graphs. Electron. J. Combin., 21(4), (2014), 31] and the papers cited therein.