We present a theoretical study of the Faraday effect in hybrid magneto-plasmonic crystals that consist of Au-Co-Au perforated membranes with a periodic array of sub-wavelength holes. We show that in these hybrid systems the interplay between the extraordinary optical transmission and the magneto-optical activity leads to a resonant enhancement of the Faraday rotation, as compared to purely ferromagnetic membranes. In particular, we determine the geometrical parameters for which this enhancement is optimized and show that the inclusion of a noble metal like Au dramatically increases the Faraday rotation over a broad bandwidth. Moreover, we show that the analysis of the Faraday rotation in these periodically perforated membranes provides a further insight into the origin of the extraordinary optical transmission.