I will be arriving in Köln (Cologne)from Brussles early in the morning and tour the cathedral and some other landmarks. Around Noon I want to take a Cruise and see castles. Are there any Rhine River Cruises that go downstream from Köln (Cologne) to a good location to catch a train to Munich?
The Rhine river is most exciting in between St. Goar and Bingen. So from Cologne I'd take a regional train to Koblenz and embark the ship there. Then sail upstream to Bingen or even Mainz. Mainz is the best point to get a good connection to Munich via Frankfurt Central Station OR Frankfurt Airport.
K-D (Köln-Düsseldorf, www.k-d.de) ship line is probably the major ship line on the Rhine in that region. However, they do not have a ship connection daily UPSTREAM from Köln to Mainz. It is very slow upstream against the current. The only ship leaving Köln does so at 9:30 and does not go as far as Koblenz. I suggest you take the train to St. Goar, then the ship from there to Bacharach. That is the most interesting part of the Rhein. From Bacharach, take the train to Frankfurt Hbf and from there to Munich.
Some years ago we took a train from Heidelberg to Cologne. We were pleasantly surprised because for most of the trip the train ran parallel to the Rhine, but up on the hills above the river. We were handed a brochure with a map that named all the scenic towns and castles along the way. I suspect we had a better view from up on the hill than we would have had on a river cruise. Plus it was a very hot, sunny day, and we were in a comfortable airconditioned train as compared to sitting on the open deck of a cruise boat. The trip by train is, obviously, much faster, and would take you directly to any number of easy connections to Munich.
Andreas gave you the best advice and use the K-D cruise. Wonderful river trips.
You should train south to St. Goar and proceed to Bacharach or Bingen - the last really scenic spot on the river - by boat - then take a train from there. The boat trip to Mainz from Bingen is a long yawner.