With a Luggage Rack
If you have a luggage rack with cross-members, a simple solution is to obtain a couple of foam "swim noodles" at Wal-Mart or Target or any place that sells swimming pool toys and supplies. Buy the kind with the hollow center. Cut the noodles to the length of the luggage rack top bar, then using a sharp knife split the noodles down the center. Pull them apart and wrap them over the luggage rack cross-members. Secure the foam with duct tape or 3 zip ties to insure it won't move around. After that bungee the canoe upside down on top of the padded cross members as described below.
Bare Car Top
The problem with securing a canoe to a bare car top is preventing scratching and abrasions of the paint. Again, the highly useful foam swim noodle comes to the rescue. Get two to four foam noodles with hollow centers. Use a sharp knife and split them down the middle. Now pull apart the noodles and bite them over the gunwales (sides) and thwarts (cross supports) of the canoe. This pads all parts of the canoe that will come in contact with the roof of the car.
Use duct tape to hold the noodles in place while loading the canoe. Securing the canoe will secure the foam between the canoe and car top.
Securing the Canoe for Travel
Lift the canoe upside down and set it on the roof of the car. Make sure that any part of the canoe that touches the roof is padded by the foam noodles. The best ties for car-topping a canoe are those yellow and orange straps with the built-in winch hooks. Attach one to either bumper or to the manufacturer's tow hook located on the frame under the car. Most cars have them.
Loop the center of the strap through the loops on the ends of the canoe where you attach ropes. If the loop is too small, tie a rope loop for the strap. Winch the front end of the canoe down tight. Attach a strap tie-down to the end of the canoe at the back the same way and cinch it down. Re-tighten the front strap and the canoe will be secure.
If there are rain gutters over your windows, you may be able to hook a few bungee cords over the middle for added security. Stop and check periodically to ensure the tie-downs haven't come loose.