On average, once a train breaks the 4 or 5 hour trip threshold a flight takes no longer door to door.
FLY
Taxi to Airport 40 minutes + Early Arrival 90 minutes + flight time 90 minutes + deplane get luggage 40 minutes + taxi to hotel 30 minutes = 290 minutes = 4.83 hours, lets call it 5 hours
EDIT ...........OOOPS, Thank you Badger, I left out the train to Salzburg. Big deal. So another 90 min for the train ride and 30 to get to the train station. So* 7 hours total I think is more than generous if the arrival time by plane and the train departure time line up well. If not, then maybe sitting on a train for 8 solid hours is the best way to go. I just did a couple of train trips longer than 8 hours and .... well I want to say never again, but I know I will be back on those trains later this year. But never my first choice. Much rather be moving around than sitting in the corner for 8 hours.
TRAIN
Taxi to train station 15 minutes + Early Arrival (yes, you can show up 5 minutes early, but who does that who also asks these questions) 30 minutes + train time 480 minutes + taxi to hotel 30 minutes = 555 minutes = 9.25 hours AND, I would check the prices on the French rail site if that is where the train originates https://www.sncf-connect.com. Second option would be OBB the Austrian company https://www.oebb.at
So, even if you do fudge the numbers and round up and down Flying is half the time; a 4 or 5 hour savings. But flying is more expensive cause taxis will cost you more and the plane ticket will cost you about 50 euro more. I am guessing if you travel light the plane will end up costing 100 euro more than a train, 200 euro more if you travel heavy.
How large is Munich airport? By passengers handled Munich is currently the 10th largest in Europe. It handles about half those handled by number 1 (Heathrow) but a tad more than half that are handled by Chucky D.