The relationship between the structural connectivity (SC) and functional connectivity (FC) of neural systems is of central importance in brain network science. It is an open question, however, how the SC-FC relationship depends on specific topological features of brain networks or the models used for describing neural dynamics. Using a basic but general model of discrete excitable units that follow a susceptible-excited-refractory activity cycle (SER model), we here analyze how the network activity patterns underlying functional connectivity are shaped by the characteristic topological features of the network. We develop an analytical framework for describing the contribution of essential topological elements, such as common inputs and pacemakers, to the coactivation of nodes, and demonstrate the validity of the approach by comparison of the analytical predictions with numerical simulations of various exemplar networks. The present analytic framework may serve as an initial step for the mechanistic understanding of the contributions of brain network topology to brain dynamics.