Oh is it, train is 5.5 hours but flight is only 1 hour (+2.5 hours for airport overhead) so 3.5 hours.
Is bus a popular option? Is that a better option than train? Faster?
This comparison of travel times is a little unrealistic. You don't want to miss your flight, so you will leave the center of Prague at least 2 hours before departure. One hour flight, 1.5 hours
from landing to the center of Munich. That's about the travel time of the bus and only one hour faster than the train, but much less comfortable.
However, there are currently not many buses between Munich and Prague. But from June 3 RegioJet will resume its two daily services (9:30 and 16:30), so that, together with Flixbusses, there will be a travel option approximately every hour. For details, cf. busradar.com (time tables
for 3 months out).