Yes it can pass, and will have the linear polarization of the filter. However, what they do in 3D movie goggles is to put in front of the linear polarizer a quarter wave filter. This polarizes the light in a specific direction, perpendicular relative to each eye.
This ensures that the circularly polarized light of each image passes only to one eye. Otherwise you will see a double image, because each linear polarizer will let light pass from both images (although with a different polarization) so it will be visible and you will no longer perceive a 3D image
