I agree with hyperlinks and probably menus & the terminal (unless you consider it a representation of the old school console terminal PCs of the 70s and 80s) having no real life equivalent. However, folder icons would be symbolic of a real world example though. Even a dock is sort of a facsimile of having things laid out in front of you on an actual desk.

The OS X deck is 3D since Leopard, but it used to just be a rectangular array of clickable pictures. With little triangles under the "open" ones.

Humans adapt. People who grew up with console terminal interfaces find them more usable than point-and-click interfaces. The assumption that common people will be all confused and miserable if you take away the bevels from buttons seems kind of unimaginative.