I usually encourage folks to be very careful with roof rack tiedowns. When it's very hot out or if the paint is fairly fresh a tight bungy cord can do a tremendous amount of damage to the paint and filler.
I encourage folks to be very careful about cartopping. Cars with short roof lines or very small spacing between the cross rails (think Subaru) are invitations to disaster. High winds, highways and high speeds can be canoe wreckers. By good quality cartopping gear and use it properly.
I am also very careful to pull boats out of the water when they are not being used. A change in water levels or wind direction can results in all kinds of damage if your boat ends up against rocks.
I do not like to carry boats from under the decks. If there are not carry thwarts I prefer to hold the canoe under the hull (if you have help) or toss it up on my shoulders and carry it properly. I have seen quite a few split decks that were caused by using them as a carry point.
Improper storage is probably the biggest cause of damage. To that point, leaving a canoe on saw horses bottom side up for a long time is not a good idea. They hog. I try to store my canoes right side up.
That said, unless it's a one in a million rare as hens teeth boat, they are made to be used. If you crack a rib, tear the canvas in the heat of combat, so be it. It's all repairable.