I use a plastic tube the pack rod came in. I'd think the issue wouldn't be padding so much as it would be protection from however you tie the rod to the pack. Keeping the rod from being snapped seems to me the challenge.
That said, last trip I had the collapsible ten dollar pole and reel tucked in the straps along the back of my Nimbus Ozone, ready for action. I didn't even strap it tightly, hooked the reel over the bottom strap to keep it from sliding out. I was hiking through a series of lakes and we stopped at each one to take pictures and cast a few - some nice brooks and rainbows hitting on my fly out there.