Could anyone suggest the best way to travel from Munich Airport to Prague? We will be traveling in late August. Thank you.
You could go into Munich, to the bus station (ZOB) at Hackerbrücke S-Bahnhof, and take the IC bus non-stop to Prague. You can do that with a discounted, advance purchase ticket (but you risk the chance of your plane being late). Be sure to specified "Muenchen Flughafen" to "Prague" when looking for the ticket so the S-Bahn will be covered too. I don't know if they still do it, but at one time the last bus of the day also stopped at the airport. Update: Still does. The 5 pm (17:00) bus from Hackerbrücke stops at the airport at 17:45 on the way to Prague.
You can also take the bus to Freising Bahnhof and catch one of the four direct ALX trains going to Prague, with a fully flexible, Bayern-Böhmen-Ticket. It takes about an hour longer, but no risk of losing your ticket if the flight is late.