In many biology, fluid transport often emerges from the coordinated activity of thousands of multi-ciliated cells, each containing hundreds of cilia. Given the sheer number of cilia in these system, a continuum theory is needed to fully analyze large ciliary carpets. Here, we formulate a continuum theory by systematically coarse graining a simple model for cilia that treats them as immersed spheres forced along circular trajectories above a surface. We analyze the stability of isotropic and synchronized states and show that they are unstable to small perturbations, which implies dynamic pattern formation. To challenge the theory, we performed numerical simulations on discrete systems. We report quantitative agreement between theory and in-silico experiments.