Wow there are so many incorrect answers and not very ELI5 answers here…
Firstly, when light enters glass (or any object), it interacts with a LOT of the atoms and even kinda “bounces around”. This is a gross oversimplification that relativity explains a bit more, but this is why light “slows down” when it enters glass. It doesn’t have to do with its atomic structure or shape.
We can observe this slowing down effect with Pink Floyd’s famous cover art. The light with more energy will be slowed down a little less than the light with less energy, and you’ll see white light break up into all of its components.
But why does the light pass through? Well in some materials, the atoms don’t have much need to capture that photon (light particle), and it’ll just bounce away. Glass happens to be one of those materials. There are other materials that really DO want to capture that photon, and usually store it in the form of heat.
If you put a metal cup and glass cup out in the sun, one of them will get really hot. Even a wooden one will get hotter than a glass one.
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