We will be going from Dusseldorf on a Sunday with the final destination Munich. On our journey we would like to take a river cruise and see the Marksburg Castle. Is it a good idea to take a train from Dusseldorf to Brauback, view the castle and town, stay over night and then take the KD boat to either Bingen or Rudeshelm and take a train from there to Munich? We will have luggage which makes it difficult to get around. I understand there are places to leave luggage in some towns, but not on a Sunday.
That is reasonable to do. Are you arriving at Duesseldorf Airport or will you be in Duesseldorf already?
If you get a hotel in Braubach, you can leave luggage there, even if you arrive too early to get into your room.
The first KD boat going up-river is at 10:05, and it is the restored paddle-wheel boat. Up-river is a little slower than down-river, but that is fine. Gets to Bingen at 15:00 and Ruedesheim at 15:15.
What is your travel date? You might find less expensive advance purchase train tickets either from Ruedesheim or Bingen depending on your travel date. Still, it will be after 20:00 before you arrive in Munich.
Maybe it doesn't matter to you, but the train is so much faster than the boat, in either direction, that there's no real penalty for training to Bingen for a downstream boat, and going to Munich from, say Boppard, which is an attractive place itself. Make sure you have the seasonal boat timetable (online) and use your train ticket for a boat discount.
Because you mentioned Sunday, note that many first Sundays of the month, Düsseldorf has a splendid outdoor riverside walk-party called Fischmarkt Düsseldorf. Not just wurst and fish, but wine, quarkbollen, beer, live music, and more. They have a Facebook page, but I'm not on Facebook. I really enjoyed it last August, and I'm not a big fan of drunken brawls. It wasn't like that at all.