The Transparency of Photons

Atoms tend to bond with their outermost electrons. So from the point of view of a photon, it really is hitting a wall of electrons that it can't find a way around unless you like physically punch holes in it. If you're a neutrino, for example, and you don't feel electric charge, then the fact that there are electromagnetic fields all through these materials is relevant to you and you pass right through it. And transparency comes down to whether you interact with the material there or not.