I agree that flying to Munich, then by train to Salzburg is the way to go. As a matter of fact, my wife and I will be doing just that in May. It is very easy! When you arrive at the airport in Munich, purchase your Bavaria (Bayern) ticket. It can also be used for local transportation in
Munich. Take the S-Bahn from the airport to Munich Ostbahnhof (East train station), and transfer to a Regional train to Salzburg. Note: When using the Bayern Ticket, you cannot use the fast EC/IC trains, only the local/ regional ones. Find more info on the DB website, www.bahn.de. The ticket is valid all the way to Salzburg. When in Salzburg, purchase a day pass for their transportation system. It will save you some money. Also, the Salzburg Card is a good deal- attractions and transportation included in the price. There are some great guesthouses on Moosstrasse for around 50-60 Euros for 2 people, breakfast included. Gute Reise!