The flyrod is my primary rod when I travel to the BW's, it's not a matter of it being a "better" rod for trolling, it is just usually the one I have rigged up.  As far as trolling, It's not my primary fishing method, I prefer casting, but If I am in travel mode, why not drape a line out behind me?   I've picked up some nice pike this way.    If I am on an unfamiliar lake, it's a great way to find weed beds/reefs etc.

Mike