Here's how it was explained to me years ago - Let's take a zinc-based base paint for instance. The zinc particles suspended in the paint is basically shaped like flakes, and when the paint is applied and dries these flakes settle in like overlapping roof shingles. The shingles then form sort of a labyrinth that becomes real hard for water molecules/oxygen to navigate. And if it can't reach the metal, the metal can't rust.
This approach works well for non-transparent paints, and there are several materials that'll form useful flakes.
But if you want to go transparent, you'll have to find another way to make the paint impermeable on the molecular level.