I would like to expand a bit on the weather vane issue that Roger mentions above.
A weather vane works because it pivots around one point that is forward of center, and generally the vane is flat, or nearly so. When a vane momentarily gets sideways to the wind, the sideways force of the wind is greater on the larger rear part of the vane than on the smaller front part of the vane, and the rear of the vane is pushed back so the entire vane is oriented again with the wind stream.
However, a car-topped canoe is unlike a proper weather vane in two ways. First, there is more than one potential pivot point -- usually two at the two cross bars where the canoe should be strapped down, and even more if any of the points where the canoe is fastened to the rack and/or rack is fastened to the car are loose. Second, and more important as discussed below, the canoe is not flat like a proper vane, but is, of course, canoe-shaped.
The sketches below approximate very roughly a 16’ canoe carried on bars about 40” apart. The left-hand sketch shows the canoe centered, with the overhang the same, front to rear. With the canoe properly aligned with the airflow of the moving car as in the left-hand sketch, wind pressure is about the same on both sides of the canoe, and all is well if the position of the canoe is undisturbed. However, if your vehicle has a short space between the bars (38” maximum on my Outback), there can be quite a long lever arm (about 77” for our 16’ canoe) ahead of the front bar, which the wind can use to exert a lot of force shifting the front of canoe sideways if the canoe gets even a bit out of line. At the rear, there is a lever arm of equal length, but because of the shape of the canoe, the air stream exerts virtually no lateral corrective force.
Various forces are constantly attempting to move the canoe out of line -- shocks and vibrations from the road, gusts and blasts of cross-winds, heavy rains, and buffeting turbulence from large trucks -- all work to disrupt the security of the canoe.
The middle sketch shows how a canoe that has become skewed on the rack is affected by the wind. It is clear that the force of the air stream around the canoe is pushing the front of the canoe to the left -- and because the canoe is canoe-shaped, there is effectively
no countervailing wind pressure at the rear of the canoe. Indeed, the canoe is actually the reverse of a weather vane.
There are three steps that are readily taken to reduce the reverse weather vane effect.
First, move the canoe more to the rear. The right-hand sketch above shows how this reduces the lever arm that the wind uses to twist the canoe -- the sketched red line indicates that there is less area forward of the pivot point for the air stream to exert force upon.
Second, use load stops on the crossbars. These strongly resist sideways motion and keep the canoe properly aligned fore-and-aft in the air stream, and once set, they also make lining the canoe up when loading and reloading much easier.
They vastly improve the lateral stability and security of the canoe on the rack when compared to just straps alone.
Both Yakima and Thule have them:
https://www.yakima.com/loadstop and
https://www.thule.com/en-us/us/roof-rack/accessories/thule-aero-load-stops-4-502-_-1683229
Stops can readily be improvised for other racks.
Third, run tie-down lines from the canoe bow to anchor points at the front of your vehicle. Two lines, one to each side of the front of the vehicle are best, with triangulation giving more lateral stability than a single line can give (green lines on the left sketch), but even a single line will help greatly to keep the canoe pointed forward into the air stream (right sketch), and can act as a forward pivot point in some situations, reducing or eliminating the reverse vane effect. And in the event of some catastrophe, the lines will keep the canoe with your car rather than creating havoc by flying loose. A line at the rear of the car to the stern of the canoe is also helpful, but having the line at the front is most important.
For purposes of illustrations, the sketches show the canoe being seriously out of line, but the reverse weather vane effect is the same, if less severe, even if the canoe is only slightly out of line in the air stream.
Most vehicles, even big ones, should use front tie-down lines. I took a walk in my neighborhood where most everybody parks on the street, and looked at a couple of dozen cars/minivans/SUVs with roof racks or rails for racks. The great majority of all makes could separate their rack cross bars by no more than 40-42 inches, even on larger cars. A few cars were in the mid-40 inches -- e.g., the Mitsubishi Outlander and the Subaru Forrester. Separation on a large Mercedes SUV was about 50 inches, on a larger Chrysler Town and County about 53 inches, and surprisingly, on a small Kia Rondo about 50 inches. The cross bar spacing of most vehicles, then, will result in significant canoe overhangs of about 6 feet front and rear for a 16 foot canoe. The greatest bar separation I found was on a Volvo wagon, at 78" -- and that would still give overhangs just a bit shy of 5 feet.
If you car-top your canoe on any standard vehicle, even a big one, I think you should use a front tie down for any trip beyond a slow, short cross-town jaunt, and certainly for any trip that involves highway speeds. If you can, move the canoe back a bit -- have it hang a little extra off the back. And get load stops for your cross bars -- they add a surprising amount of stability and security.