Bacharach/St Goar or Rothenburg

Rothenburg only takes a few hours. Same for Bacharach/St. Goar... but the Rhine offers so much more to see and do besides these 2 towns and is so much closer to FRA airport that I think it's a no-brainer.

In between Bacharach and St. Goar is Oberwesel. Besides walking the town wall you can hike up through vineyards to the Günderodehaus if you have time:
https://images.robertharding.com/preview/RM/RH/VERTICAL/832-149969.jpg
http://www.christiane-geldmacher.de/wp-content/uploads/2014/09/rhein2014-003.jpg

North of St. Goar is Boppard:
http://home.kpn.nl/JLKampen1961/alb/Rome/Pauze%20in%20Boppard.jpg
http://schnuggel-elsje.de/upload/Bilder/IMG_0131.JPG
http://ext.pimg.tw/samlucky5711/1379089584-1923285561.jpg?v=1379089585 (Gedeonseck Terrace, short walk from top of chairlift ride.)
Boppard has lots of nice places to wine and dine:
http://www.deutschlandgourmet.info/bilder/gross/5710-Restaurant-Weinhaus-Heilig-Grab-Boppard.jpg
https://upload.wikimedia.org/wikipedia/commons/9/97/Boppard_Weinhaus_R%C3%B6merburg.JPG

Opposite Boppard and north is the town of Braubach and Marksburg Castle, the only never-destroyed medieval Rhine Castle you can tour.

In between the Rhine towns and FRA is MAINZ. It's just 25 minutes from FRA by direct train if you need to sleep near the airport - and it's a very nice city to visit anyway, if you have the time.

Rothenburg would not be worth it compared to either of the other options, whatever time of year it is.

The Rheinfels castle ruin at St. Goar is one of my favorite sights on the Rhein. I also like a walk along the Rhein at that point. I like the walk up to the hostel at Bacharach past the chapel ruins. I would find these two towns a full two days and it is closer to the Frankfurt airport.

While I would prefer the Rhein in your case, I still like Rothenburg for two days. I like the Stadtmuseum with its landscape paintings, the altar in the Franziskanerkirche (Franciscan Church) by a young Tillman Riemenschneider, and a walk into the Tauber Valley to Detwang to visit the small Peter and Paul church with a more polished Riemenschneider altar. The views of Tauber valley from the town gardens and from the walk outside the wall are quite spectacular. Rothenburg is still one of my favorite places to visit in Germany, even with the gaggle of tourists in the town square. You just have to walk a few steps away from the center to get a good feel of the place. Plus Rothenburg is quite quiet and pleasant in the evening after the tour buses have left.

Lubitsch has made some good suggestions as well, but I think your two original choices are legitimate considerations, and I do not think you or anyone else here is reducing the whole country to a few sights. You are just reducing your travel radius from FRA based on your 2-day restriction - a wise thing to do, and no mistake at all. You'll likely have a nice time, whatever you choose.

Lubitsch writes that Rick's "...book most certainly narrows Germany down to a handful of places..."
Yes, it absolutely does. There's a LOT more to Germany than you can find in Rick's book alone. I guess with the word "you," Lubitsch was actually addressing RICK - to give him credit for that reductionism/"mistake" - not YOU, dwest.

Pleased to hear you've taken rehab step #1, Lubitsch.

And... your bit on RS Germany is of course accurate (the only possible analysis, actually, for those who know Germany.)

Lubitsch, Rick Steves' guidebooks are intentionally written for first-time American tourists who have only a limited time to see a country, and want to see the highlights. So yes, he does focus on those areas and towns that are most popular and hopefully creates an interest for seeing more, on your own.

I recently bought one of the RS guides because I was curious what I would find there and I'm still shocked. It's all about big towns and he has otherwise only Berchtesgaden and Füssen, some towns along the Romantic Road, the Middle Rhine valley and some Moselle towns (which are particularily poor choices) plus finally the bizarre choices in the Black Forest area

That was my criticism for several years, but to be fair, recent additions of his guidebook have branched out far more. Circa 2010, the Blue Book probably didn't even include the word "Thüringen", now he has added several locations in that state. But despite what some posters here may claim, RS books really aren't written for people who have made multiple trips. Rather, he's more like a friendly face to gently hold the hand of first-time visitors until they find their own footing. I too really enjoyed his books in the formative years of my traveling experiences, but now that I've made two dozen trips and lived on the continent for several years, he really has nothing to offer me anymore. I still enjoy reading what he has to say about places I already know well, but I no longer rely on him for primary recommendations.

I would choose Bacharach/St Goar. Rheinfels Castle is one of my favorites. I must admit though, that I've never actually stepped foot in Rothenburg. We drove to it one year, saw the tour buses and crowds, and kept on driving!

I too, recommend going to Büdingen. It cuts down on your travel time and you don't have a lot of excess time anyway. The town is a gem and combined with its' almost neighbor, Gelnhausen, you have a great day trip.