Actually, there are direct ALX trains between Munich and Prag every two hours, starting from Munich at 4:43 and from Prag at 5:33 - eight per day in each direction. They each take just under 6 hours. After 9 AM workdays or anytime on weekend days, you can use a 28€ Bayern-Böhmen-Ticket for one person between Munich and Pilsen, but you will need a Czech Rail ticket between Pilsen and Prague for 105 Kc (about 4 euro) each way.
You can also purchase just a Prag-Spezial round trip ticket from the Bahn for 65 euro per person (from Munich to Prague).
And, there is a non-stop Bahn Fernbus between Munich ZOB (at Hackerbrücke) and Prague. It's about an hour faster, but the full fare is almost 70 euro, one way. Advance purchase discounted tickets are available for as low as 20 euro, but you must commit early to a specific (date & time) bus.