After a stay in Munich, I have 4 nights and 5 days to see Fussen, Rothenburg, Cochem areas. Is Rothenburg worth spending the night or can it be explored in a few hours on the way to Cochem? Are Fussen and Cochem worth the 2 nights each? Are "late" check-ins an option when staying at a B&B?
Regarding Rothenburg, it can be "seen" in 4 hours if that is all the time you have. I stayed the night there last year and enjoyed taking the night watchmens tour and walking the streets and wall at night. It really depends on what you are wanting to get out of your trip to Rothenburg. For me it was a rest from big, faster paced cities.
I have not been to Cochem yet, so I don't know what you would be giving up by staying in Rothenburg. I know that I would do it again.
I would spend the night in Rothenburg, it is really nice when the buses leave.
As far as Fussen is concerned unless you are doing day trips and using it as a base I think 1 night is enough.
I would be more inclined to treat Fussen as a day trip rather than Rothenberg. The nightwatchman's tour is well worth the night in Rothenburg and we relaxed there taking in the little beer gardens. I have not been to Cochem - so I cannot comment on that one.
Of the three, Cochem is the nicest place to stay awhile. You can catch a train down to Trier for a walk through the town and Roman ruins, you can see Burg Eltz (if you like to walk, the walk from the train station in Moselkern(?) is great), you can tour Cochem Castle or you can relaz at a wein stube.
I would opt for a night in Rhotenburg simply to enjoy it without the daily tours. The nightwatchman's tour was enjoyed by our entire family.
Fussen is really just a base to see Neuschwanstein and surrounding area. Of the three, I would spend the least time here unless you have plans for the area.
As far as late check ins go - I always call the place and let them know when I'll be arriving so they don't worry that I'm not coming. A late check-in of 5 or 6 pm probably isn't a problem if you let them know you're on your way and when you will arrive. After 8 pm, I think you would be pushing it but still may be okay depending on the owners.