Why is Graphene Transparent?

Graphene is only transparent because it is very thin (one atom thick). If it absorbs 2% per layer then just a few hundred layers would absorb almost all light and that would still be a very thin sheet of graphite.

The question should be why does graphene absorb so much light compared to diamond which really is transparent? A simplified answer is that graphene is a very good conductor because it has only three covalent bonds per atom compared to the full four in diamond. This makes it possible for electrons to move freely over a sheet of graphene to conduct electricity. Like metals this means it will absorb or reflect light because the free electrons can absorb the small amount of energy in the photon. In diamond the photons would need to have enough energy to release an electron from the covalent bonds. For visible light this is not possible so the photons pass right through the diamond and are only stopped or deflected by impurities.

I assume the biggest factor is the thickness. Graphene is a layer of carbon one atom thick. Light is absorbed/reflected by the top layers of a material and if you make any material into a layer one atom thick you'll find it increases transparency a lot.

The thing that is special about graphene is that it forms bonds in a 2D layer where most materials don't.