As phasor measurement units (PMUs) become more widely used in transmission power systems, a fast state estimation (SE) algorithm that can take advantage of their high sample rates is needed. To accomplish this, we present a method that uses graph neural networks (GNNs) to learn complex bus voltage estimates from PMU voltage and current measurements. We propose an original implementation of GNNs over the power system's factor graph to simplify the integration of various types and quantities of measurements on power system buses and branches. Furthermore, we augment the factor graph to improve the robustness of GNN predictions. This model is highly efficient and scalable, as its computational complexity is linear with respect to the number of nodes in the power system. Training and test examples were generated by randomly sampling sets of power system measurements and annotated with the exact solutions of linear SE with PMUs. The numerical results demonstrate that the GNN model provides an accurate approximation of the SE solutions. Furthermore, errors caused by PMU malfunctions or communication failures that would normally make the SE problem unobservable have a local effect and do not deteriorate the results in the rest of the power system.