The traditional offering is five yen because that's "go-en" in Japanese, which could also mean "good connection/good luck". Plus it's a trivial amount of money, so people can afford to give it whenever they go to a shrine.

Shrines do, I believe, tend to prefer larger offerings. 500 yen is a lot for an ordinary visit, however.

(Incidentally, Japan still has one yen coins. They are small, and so light that one will sit on the head of a pint of Guinness.)