I have taken a piece of PVC that will slide inside the tube and cut it so that it sits about 8 inches above the top of the stainless tube. In the PVC, I cut a deep slit to hold the fly reel. By wedging the PVC pipe into the rod holder, it becomes a stable place to store the rod. For extra security, you could add a strap above the reel to hold the rod into the pvc. Here's what it looks like on my yak:
Well, I'm on the Downeaster Alexa, and I'm cruisin' through Block Island Sound.
I have chartered a course for the Vineyard, but tonight I am Nantucket bound.
-Billy Joel "Downeaster Alexa"