I understand better now.
If you plan to do Brugge and/or Ghent from Brussels -- which is very easy, by the way - then you original thought is probably a good one.
There is plenty to do on the Rhine/Cologne/Frankfurt area for 3 days -- in fact, the reason I steered you away from the area -- is because 3 days will just get you started down there. If you do go down, don't do Koblenz as a day trip -- do plan to stay somewhere on the Rhine.
A possible way to link those destinations...
Day 1: Morning train Amsterdam-Cologne (2 1/2 - 4 hrs). Lunch in Cologne, Cathedral - back on train in about 3 hrs to destination on the Rhine (1 hr). Stay on the Rhine. (I've only stayed in St. Goar, but Bacharach is a more popular choice.)
Day 2: Rhine day. Take the boat downstream and ride the train back to where you started. See some castles, don't miss the tunnels below Rheinfels Castle in St. Goar. Evening train to Frankfurt or Wurzburg (2 - 3 1/2 hrs, 2-3 changes).
Day 3: Day in Wurzburg or Frankfurt. Evening train to Brussels (4-5 hrs, 3-4 changes).
That's just a possible. Between Frankfurt and Wurzburg, with 1 day to use, I would choose Wurzburg. It is a very enjoyable city, see the Residenz, and can give you a good taste of a modest sized German city in 1 day. Frankfurt's a lot to take in within 1 day.
I didn't check it -- but this might make more sense in the reverse order. Amsterdam-WurzburgOrFrankfurt-Rhine-Cologne-Brussels.