You were assulted in your car and told by police you need to file charges at local magistrate instead of them finding and arresting him you have a witness Why would the police not arrest him?

I don't know what jurisdiction you live in and it differs sometimes quite a bit. As a general rule unless the Officer witnessed the assault, it is standard procedure to refer them to a magistrate. If they personally witness a crime they usually make a "on view" arrest. Things occurring outside the officer's presence are usually referred to a magistrate who requires the complaining witness or officer to sign a formal complaint charging someone with the crime based on either personal knowledge or probable cause. The local prosecutor and magistrate usually have access to the report made by the officer to aid them in drafting the correct charge. Then a warrant to arrest the individual is issued and the officers execute it.