I routinely carry two 18' sea kayaks on my Prius - Yakima rack. No issues except my mpg goes down to the low 40's. I've considered a lightweight trailer to see if it would help with the fuel efficiency, but am concerned about voiding the warranty.

The Civic or Prius should do fine with the canoe - also a lot easier to put on the roof than with an SUV. Just make sure you get a quality rack - both Thule and Yakima are good.

Cheers, Will