Having worked 6 years at a canoe & kayak rental, as well as raced canoes, this is my advice.
You can carry a kayak on a factory rack given the following:
1. Your rack is down TIGHT (the dial knobs)
2. You use proper straps such as thule, Carlisle, and a few others with buckles that you can pull tight against...you could use ratchet straps, but I like the kayak specific straps as you get a fully closed loop and not a hook that may or may not slip off.
3. As previously stated, put some foam down. Not only does it protect your boat and your car, but using even something as simple as a pool noodle cut and wrapped about your load bar with all the kayak to seat a lot better than it would against a flat bar. But also, as stated about, the J hook kayak racks make good contact with the boat.
4. This is likely the most important, and I am sure people will disagree with me, but this is my advice.... You haul using your factory rack short distances and not on free ways. Going 70 mph and catching a gust of 30 mph makes that kayak a large sail against 100 mph wind, and personally I don't think those knobs are all that secure. I would not hesitate to use the factory rack up to 55 mph over short distances, though.