I concur with cygnus on not driving - I might want to do the drive in a different season, but in November there's always the chance of inclement weather (at which time the autobahn speeds may be restricted).

Taking the train offers city-center to city-center transportation on very comfortable trains (ICE), while flying offers overall less travel time (keep in mind that TXL is close-in, while MUC is a fair distance from the city center, although the S-Bahn offers good connections to central Munich).