I use trains in Germany almost every month, but have not used Rail&Fly.
Having said that, CGN is the Cologne airport. I assume the train does not go there, but to the Cologne main station (Hauptbahnhof).
The train from FRA airport to CGN (airport) requires a train change usually at Cologne-Deutz. (one station away from the main station)

As said above, I check the seat chart a day before I go. If it looks pretty booked, and the ride is 2 hours or more, I grab a seat and pay the 5.50.
There are other factors, of course, how much luggage you have, do you have kids in tow etc.