We have developed a multi-scale model for organic-inorganic hybrid perovskites (HPs) that applies quantum mechanical (QM) calculations of small HP supercell models to large coarse-grained structures. With a mixed quantum-classical hopping model, we have studied the effects of cation disorder on charge mobilities in HPs, which is a key feature to optimize their photovoltaic performance. Our multi-scale model parametrizes the interaction between neighboring methylammonium cations (MA+) in the prototypical HP material, methylammonium lead triiodide (CH3NH3PbI3, or MAPbI3). For the charge mobility analysis with our hopping model, we solved the QM site-to-site hopping probabilities analytically and computed the nearest-neighbor electronic coupling energies from the band structure of MAPbI3 with density-functional theory. We investigated the charge mobility in various MAPbI3 supercell models of ordered and disordered MA+ cations. Our results indicate a structure-dependent mobility, in the range of 50-66 cm2 V-1 s-1, with the highest observed in the ordered tetragonal phase.