I think it's ultimately a matter of semantics. Somewhere along the way, "you" became a colloquial "I". In some bizarre way, I often find "you" being used when telling people how to do things, or more specifically how you yourself do things. Seems a bit ironic at times, but people usually understand that you're referring to yourself. When you refer to yourself as "you" in your head, perhaps from a psychological perspective it might stem from the way you view yourself. Even when alone with your own thoughts, your brain might be most comfortable with that subject-object relationship that it's used to dealing with. You may be alone with your thoughts, but your brain still needs someone to talk to, even if it's itself.
"Science without religion is lame. Religion without science is blind" - Albert Einstein
"The Mighty One appears, the horizon shines. Atum appears on the smell of his censing, the Sunshine- god has risen in the sky, the Mansion of the pyramidion is in joy and all its inmates are assembled, a voice calls out within the shrine, shouting reverberates around the Netherworld." - Egyptian Book of the Dead
"Man fears time, but time fears the Pyramids" - 9th century Arab proverb