arriving in Salzburg at 4:00am - safe?

I think the biggest danger you face at that time of morning is dying of boredom. According to the Austrian Rail website, there is a first class lounge in the Salzburg Hbf. It opens at 5:30 on weekdays, 6:30 weekends and holidays. Access is available to anyone with a first class Eurail pass for Austria. Access is also available to anyone with "any type of sleeper cabin ticket ... on the day of arrival up to 2 hours after the actual arrival".

I'd say yes. The station as I recall is a bit outside of the historic area (its a walk but not super far). I boarded a night train there a few years back and didn't feel even remotely unsafe. Generally European stations are in good areas and are safe. You might see an occasional homeless person, but they're much safer than what you find in the states. If you feel nervous just have someone in the ticket office call you a cab and head towards town. Some coffee shops open early and you could ask your cabbie to drive you to one. I've only felt unsafe a few times in LARGE european stations (Frankfurt and Naples were the only ones) but never in Austria.