Help with Itinerary - Munich and Salzburg and Rothenburg

Rothenburg and Munich aren't neighbors. Rothenburg is actually closer to Frankfurt by about 20 km.

With 5 days, why drive all across Bavaria for Rothenburg? Why not just have yourselves a nice time in Munich and Salzburg? If you want to see a smaller attractive Bavarian town, you could do a side trip from Salzburg to Berchtesgaden - it's very close.

You could also arrange on your final day to visit Freising or Landshut - both close to MUC airport. Then get to a MUC airport hotel for your final night.

Yeah, Rothenburg is pretty remote from Munich, especially using a train. If you were flying into Munich and out of Frankfurt, that would be a horse of a different color.

With only five days, I would not spend too much time traveling. I would pick 2 of the 3 and spend the last night in Freising or Munich. I like Rothenburg better than Salzburg but the train routes are more time consuming. By traveling too much, you might deny yourself the opportunity to settle-in and enjoy any of the three.

I'd skip Rothenburg. Not enough time. Plenty to see in Salzburg.

I think I'd go to Salzburg first. You're arriving in Munich in the morning, so probably won't be able to check in to a hotel before mid-afternoon. I know I am a jet-lagged zombie on arrival, so might as well be on a train for a few more hours, and keep moving forward.