Best way to travel from Munich to Salzburg

Most people use a Bayern-Ticket for Munich to Salzburg, especially if they will do any travel inside Munich. It covers both the regional train to Salzburg and all conveyance (S- & U-Bahn, trams, buses) of the MVV (Munich metro) for the day (after 9 AM workdays).

The Bayern-Ticket costs 25€ for the first person and 6€ each for persons 2 - 5.

If you don't need to use the MVV, Meridian, the private train line that runs regional trains between Munich and Salzburg has their own day pass, das Guten Tag Ticket, for 4€ less (21€ + 6€) than the Bayern-Ticket. Das Guten Tag Ticket is valid on the Meridian trains between Munich and Salzburg, but not on conveyances of the MVV.

Meridian is a private company, but it's trains run on German Rail tracks and it adheres to the German Rail regional schedule. With the exception of das Guten Tag Ticket, it's fares are the same as the Bahn's.

You can find schedule and standard fares on the German Rail website.

I took this bus it was clean efficient and it only cost 5 euros
https://www.flixbus.com/

I took this bus it was clean efficient and it only cost 5 euros

Lucky you. The present pre booking fare is €15. Please not that there are only four Flixbus connection frome the airport. Trains go at least every hour. There is no need to prebook a train. Just get a Bayern Ticket valid from 9am) from a ticket machine (€25), take the S8 to Munich East (München Ostbahnhof) and transfer to the Meridian train to Salzburg.

If you are certain enough that you can make a specific bus booking, then you could book a Savings Fare on a RailJet for 19€ and get there in 1½ hr.