I have a train getting there 2pm and leaving 11pm, are the station and the routes to the trains safe?

Yes they are

I thought the station was safe. They have security guards there.plus old Sacramento is right behind the station so i feel because of that its pretty safe for the tourists.

The station is in a dodgy area of downtown. They have a security guard that tries to keep the homeless moving on. It's fine, during the day, to walk around. Old Sacramento and the Train Museum are very close by. I would not advise leaving the station, on foot, after dark. The station has the old fashioned long wooden benches. They do have backs, but are not very comfortable for a long stint in the station.