It is said that Shinto begun at the same period as when human in Japan started having `human's mind' and having feeling of respect and reverence toward something holy.
The literal meaning of Jinja (神社) is Yashiro(社) of God(神), and it is said the word Yashiro(社) originally came from another word meaning a purified place.
In old eras, people believed that God doesn't stay at the same place, but come only during the festival. That's why they need to purify the venue every time they welcome God. There wasn't Junja as a permanent place to deify God.
It has been believed that God stays at a purified place such as a good-shaped mountains, evergreen trees, big rocks. We can find those places (Yorishiro in Japanese) hanging pieces of gold and silver paper or white paper nowadays.
*Bibliography
`Jinjatte donna tokoro ?` by Kikuyo Hisafuji (Chikuma shobo)