And it's not like we're absorbing the nonaligned portions of the photons polarization energy at each filter with individual photons.  That would create a red shift.  So I guess it's the total energy of the light wave (assuming I'm using this word right) is getting normalized to the polarization of each filter as it passes with the remaining energy absorbed by the filter.  Which I guess would mean that the filters are effectively destroying all the photons and recreating new photons that just happen to have the same statistical mix of wavelength and direction of travel, but with the new polarization mix.  Trying to make this work with classical physics is fun.