Electron transmission through a series of self-assembled monolayer films is studied using an iterative Green's function method with absorbing boundary conditions. The nuclear-electron interactions are calculated using suitable pseudopotentials, and the Hamiltonian is evaluated using a discrete variable representation. The presence of electronegative head groups on the metal surface gives rise to much lower transmission through the layers. The presence of these headgroups also produces asymmetric transmission effects where the transmission coefficient depends on the incident direction of the electron, as observed in recent STM measurements. Longer alkane chains (up to 18 carbon atoms) are more ordered due to the self-assembly process and have higher transmission coefficients at lower electron energies. This collective effect is observable experimentally and is not a property of single molecules in which transmission probabilities decay roughly exponentially with chain length.