If you gamble with the 1 hour connection, you should have a plan B in case you miss the flight. I reckon the chance of not making the flight is only 5%, but if that means buying a new ticket could be a pretty expensive.

The IC bus (operated by DB) is pretty comfortable from Munich to Prague, though a long journey on a bus. Tickets in advance are relatively cheap (but fixed against a specific bus).

The cheapest could be to buy a Bayern-Böhmen-Ticket, which will take you on regional trains (i.e. RE, Alex) from any station in Bavaria to Plzen, where you can buy another ticket to Prague (much cheaper to buy in Czech Republic than Germany). Total cost around €35~ish. The trains go slowly, but you have more space to walk around, work, watch DVD's etc.