The Bahn IC bus is the fastest way to Prague, but for walk-up tickets, it is expensive - 66,70€ per person. The train is slightly slower, but can be less for last minute travel.
There is a direct ALX train leaving Munich Hbf at 12:44 (it stops at Freising at 13:07). A Bayern-Ticket (23€ for one person) will cover the bus from the airport to Freising and the ALX train as far as Furth im Wald, at the Czech border. A Bahn ticket from Furth to Prague (purchased at the Bahn counter at the airport) is 29,30€. So that is 52,30€ for the trip.
If you purchase the ticket from Furth im Wald to Prague for that train (EC 355 Karel Čapek) from the Czech Rail website, it's only 391 Kc (14,37€), 37,37€ for the entire trip.
If you know your return date, you might get an advance purchase fare on the bus as low as 29€.