I have often towed with it on - and
gone faster than I should down the motorway (accidently of course). A cover is essential if you are carrying the wifes luggage in the boat
I use adjustable bungees
pulled tight, around every 1/2 metre. I added extra points to accomodate this. I also tape right round the bow with duct tape a couple of times (mainly because my cover is not a great fit and there is excess material at that point).
Never had any problems towing 6 hours plus.
Chaffing of tubes? Not in my experience.