My husband and I are spending a month on a driving trip through West of Germany, Holland and Brussels. We are flying into Frankfurt and was planning on getting our car there, however after a little research it sounds to me best to take the train through the Rhine valley and Mosel valley and then end it in Trier where we would pick up the car. We want to experience it the best way possible and don't know if car is best or taking the train and doing a boat ride here and there and also bike. Any suggestions?
and don't know if car is best or taking the train and doing a boat ride here and there and also bike.
All these forms of transport work depending on the situation. There are very nice bike trails along the Mosel, some in disused railway beds. There are a variety of ticket deals allowing you use of the local trains and buses for an entire day for 20 to 30 EUR for 2. A ride on a tour boat on the Rhine, between Boppard and Bingen for the most scenic parts is recommended. The fast way is with the current south to north, but then going upstream makes the scenery go by more slowly. A car can be handy at times to get to out of the way places like Burg Eltz, or staying at a small "Weingut", a winery with a few guest rooms for rent for very good prices.
"...end it in Trier where we would pick up the car."
You're leaving Germany after Trier, or ??? And will you return the car in Germany later? Expect a heavy drop-off fee if you pick up in Germany and then drop outside Germany. If you'll be traveling more in Germany there's a good chance that the train will meet your needs - Germany has a dense rail network with over 5,000 train stations.
As for using the train it's extremely easy to catch one at FRA airport for transport to the Rhine or Mosel - and a safer one as well in lieu of driving after an overnight flight.
Of course you would want to try to book accommodations within reasonable walking distance of the train stations. This is generally not a problem in the smallish Rhine/Mosel towns. There are all kinds of riverfront towns on the Mosel between Koblenz and Bullay that are served by train; from Bullay to Trier, the tracks veer away from the river; buses cover most river front towns after that.
On the Rhine, both sides of the scenic part of the river between Koblenz and Rüdesheim (or Bingen) are well served by train.
https://www.mittelrheinbahn.de/assets/images/6/MRB_Karte_Streckennetz_2018-66058e06.svg
http://www.vias-online.de/data/9_netzplan_rhg.jpg
Think of the train as your prime transportation mode - boats, which offer skimpy schedules as a rule, and bikes are for sightseeing on outings, for the most part - not transportation.