Both Inno Racks and Yakima Racks have really good solutions for a 2003 Hyundai Santa Fe kayak rack setup.
With Yakima racks you'll want to first install the Yakima RailGrab roofrack system to the Hyundai Santa Fe factory side rails. You can then mount any kayak racks to the Yakima RailGrab crossbars.
http://www.orsracksdirect.com/yakima-railgrab-roof-rack-system.html
Inno Racks probably has the best solution for you. You can install either the Inno IN-SR roofrack or IN-FR roofrack to the Sante Fe siderails. The IN-SR is a sleek looking, low profile option and the IN-FR is a more classic looking design. The IN-SR is offered in both black and silver color choices while the IN-FR is in black only. Also these roof rack systems all come with locks included so you can lock the rack to the car.
http://www.orsracksdirect.com/inno-in-sr-factory-siderails-roof-rack-system.html
http://www.orsracksdirect.com/inno-in-sr-roof-rack-silver-system.html
http://www.orsracksdirect.com/inno-in-fr-car-rack-system.html
Then you can connect the Inno INA444 locking kayak rack to the Inno base rack crossbars. This is a very cool kayak rack because it has an integrated locking system to lock the kayak to the rack.
http://www.orsracksdirect.com/inno-ina444-kayak-canoe-rack.html
Another really cool optional accessory is the Thule 854 Water Slide mat. You attach itto the rear crossbar on any of the above roof rack systems and then lay it down flat over the back of your car. It both protects your car from contact with the kayak and also helps to slide the boat up into position on the kayak rack. There is a non slip underside so the 854 Water Slide won't move around.
http://www.orsracksdirect.com/thule-854-water-slide-mat.html