We are visiting Bremen for a week and then want to explore southern Germany. Is it better to take a hopper flight to Munich from Bremen and make a driving loop (Munich, Salzburg, Fussen, Baden-Baden, Bacharach, Rothenburg, Munich) or take the drive from Bremen? If driving, where is the best place to stay between Bremen and Bacharach to break up the drive?
Third option would be to take a direct, 5.5-hour train ride from Bremen to Munich. These depart about every two hours. Relax and bring some lunch onboard. Prices depend on how early you purchase but this is one case where flights don't look much cheaper at www.skyscanner.com, from either Bremen or Hamburg.
Looking Up Train Schedules and Routes Online gives you the Deutsche Bahn train link and tips for using it.
[edited] If you're driving, you can usually drop the rental car in a different German city without any significant fee. So I would not drive a Munich-to-Munich loop. Driving Bremen-Bacharach-Rothenburg-Baden-Baden-Fuessen-Salzburg-Munich makes more sense. Or take a shorter, direct train from Bremen to Cologne or Koblenz and pick up the car there. Fuessen and Salzburg can also be done as daytrips by train from Munich, but I'd do them first with the car.