Frankfurt to Dusseldorf via Rhine River

From FRA airport: The Regionalbahnhof (regional train station, 1 of 2 airport stations) sends off direct trains to the Rhine Valley towns of Bingen, Bacharach, Oberwesel, and Boppard. RE trains leave at 13:24 and 15:24 for the trip of approximately 1 hour. (You can leave at other times in between as well - but these trains will be easiest for you since they do not require a change of train.)

You can overnight in any of these towns, ideally within walking distance of the train station. All are small towns with accommodations in reasonable locations. You should begin your room search right away as the area is very popular and a family of 4 may find limited availability. Bingen is located at the southern end of the Rhine Gorge, the zone where most people start their river cruise and also where you will have the greatest number of cruise boat options. It is also the closest to FRA airport and offers some amazing views. From the nH Bingen hotel - pictured in the previous link - you would have great views as well as the Bingen riverfront promenade and the day-cruise boat docks at your feet. Also, you can walk there from Bingen's main train station (Bingen Hbf) which is across the bridge you see in this photo. So I would start the hotel search with the nH... but there are a few other options nearby which may work for you as well.

It is the Bingen > St. Goar segment which is most scenic. See cruise zone on this map. This route takes about 1.75 hours.

If you find a room in Bingen, you can take your cruise that same afternoon, possibly (there's a 16:30 K-D cruise) - or you can cruise the next morning (9:15?) If your room is in Oberwesel or Bacharach, you should backtrack by train in the morning to Bingen to board. It is the Bingen > St. Goar segment which is most scenic. See cruise zone on this map. This route takes about 1.75 hours.

If you cruise on the second day, you may have time to tour Rheinfels Castle after stepping off the boat in St. Goar. After that, return south to Bingen (or Bacharach or Oberwesel, wherever you stayed the night) by train to fetch your bags.

If that's Bingen, I suggest you hop off the train in Bacharach (10 minutes south of St Goar) for a look at its gorgeous half-timbered buildings. Then hop back on 1 or 2 hours later and return to Bingen for your bags.

There are DIRECT IC trains from Bingen Hbf to Düsseldorf (14:07 - 16:09... or 15:07 - 17:09.) Trains from the other Rhine towns will take longer and usually require a change of train, which I would choose to avoid since delays are common these days... better a few minutes late from Bingen than 1-2 hours late from the other towns if a connection is missed!

Train and cruise boat scheduling links:

https://int.bahn.de/en/
https://www.k-d.com/fileadmin/KD_Fahrplaene/KD_Fahrplan_intern_2024_web.pdf

This is tricky, as you are arriving rather late at FRA at 12:30 pm. Ideally, you would want to catch a KD boat at either Bingen Stadt, or Ruedesheim, but the boat departure times are 14:15 and 14:30, and you can't there in time. Second best is to take a 13:24 regional train from the airport to Bacharach, arriving at 14:20 and get the 15:15 boat there to St Goar, arriving at 16:10. That is the best part of the Rhine Gorge. Then get a 16:40 train at St Goar that gets you to Duesseldorf at 19:01, after a train change in Koblenz.

I believe that this is your only reasonable way of doing this. If you cannot make the 13:24 train from FRA Regionalbahnhof, just take a train route along the Rhine to Duesseldorf and view the castles from the train car windows.

There are direct ICE trains from Muenster to FRA, where you can rent a car and return it there for your flight home.

@Sam: As I read the OP, they do not have to be in D'dorf on the day their flight arrives... Thursday night could be spent in the Rhine Gorge. There's adequate time to cruise the full scenic segment from Bingen > St Goar and to fit in some sightseeing on the ground as well.

"...we land in Frankfurt on a Thursday arriving 12:30pm and need to be in Düsseldorf by dinner (after 5pm) on Friday (the next day)."

ShannyLuo, Munster is a nice visit, but it seems like there is a lot of driving and tourism you have not including in your questions. Make sure your hotel has a place to park the car.

You have splendid answers for what you did ask about. The river itinerary you describe should be mainly done by train. The boats are too slow, too infrequent, and (except for Bingen to St. Goar/Bopppard) have too little scenery. The train is many times faster than the boat, no matter how many local stops it may make.

If you are asking, "Is there value to driving two hours from Munster to Duesseldorf?", I would say, "No." I would observe that rental cars are in demand in this high point of an already high tourist season. You need to plan your summer car pickup carefully, especially if you hope to get an automatic transmission. We returned our car far out from Frankfurt, but near the S-Bahn. I'd worry about automatic availability at suburban rental offices. We had to wait an hour for a standard-transmission sedan to be turned around for us, when I refused the giant Transit Van automatic they presented us with at FRA!

Yes, I missed the "Friday (next day)" part. Staying over first night for jet lag recovery is a good idea.

Thank you everyone for your very informative responses!