If you miss your scheduled train on a saver fare ticket, you forfeit the ticket.
Regional trains are always an option. The regional route takes you to Cologne via the Rhine River Valley, Germany's most scenic train ride.
Rhine Valley Route
Expect to spend 4 hours or so to get there this way.
A wise move, if you are planning to see the best part of the Rhine Valley, is to drop Cologne as your first destination. Stay in one of the Rhine towns in the scenic part instead, which greatly shortens this trip. Then see Cologne later. You could reach Rüdesheim, a good jumping-off point for cruises and castle tours, in just 90 minutes by regional train.
Map of the scenic Rhine Gorge area:
http://www.loreley-info.com/eng/rhein-rhine/walking-hiking.php
The fare to R'heim from FRA is €11 ea. Buy the ticket once you get to the airport's Regionalbahnhof station and hop on any of the regional trains heading to R'heim. Service is typically every 30 minutes.