If you only need to transport the kayak several times, a
may fit the bill. If you choose this option, you must tie down both bow and stern of boat, as well as the middle (through the car doors). For hood (and trunk, for sedan owners) tiedown points, home-made versions of http://www.discountramps.com/thule-hood-loop-strap.htm or http://www.discountramps.com/thule-tie-down-loops.htm can be made.
For longer term use, even the factory rack is not good. I bought a Camry wagon with a factory rack, and ended up taking it off, and installing a Yakima rack system. If you're concerned about the appearance of the vehicle, you may not want to do as I did, but if you want a rock-solid rack system for hauling boats, lumber, and anything else you can lift onto the roof, this is what you want to do:
1) remove headliner inside the car
2) remove factory rack, and plug holes where factory rack sidebars attached. I used SS bolts, fender washers, and neoprene gaskets.
3) install Yakima
toploader brackets by drilling holes throught the roof, and permanenetly mounting the brackets.
4) purchase and install Yakima racks with
1A towers. (Thule probably offer similar bolt-down brackets for their racks)
I installed three pairs of brackets on my wagon, so I can carry both short whitewater boats/bicycles, and long canoes/sea kayaks.
PM me if you'd like to see pics.