We were originally planning to take the train from Salzburg to Vienna, but found out that we can do a one day car rental with no drop charges. Got the Budget rental car delivered to the Sheraton Salzburg for free, and took about 3 hours door to door arriving in our hotel in Vienna. The rental charge was about 100 euros, including CDW at about 30 euros/day.
For two or more persons, this is certainly a viable option to the train; you also get to use the car in both cities for just a one day rental.