Went to CGN for a wedding last year.
Originally booked on TG to MUC and then flt MUC-CGN. Would have preferred this option. However, had to go to Kuwait - so ended up booking Kuwait Airways to FRA.
Took the train - not a pleasant experience on a Friday afternoon. People everywhere, and some passenger-of-size occupied my seat - did not have the heart to ask her to move. Also, there was nowhere to put my luggage, so ended up not having a seat at all for the short train journey. The positive aspect was that the train ride is fairly short indeed.
The train station in Cologne is somewhat unpleasant, but finding a taxi was not a huge issue.
I would vote for the option of flying MUC-CGN.