You should be fine as long as the kayak is strapped in properly. I used a four-point strap set-up that kept my kayak from moving front-back or side to side. Just don't leave it hanging out over the edge if it gets really hot. It doesn't take long to develop a flat spot on the hull.
I carried my Drifter in the bed of my Ranger for 4 years with only one incident. I got rear-ended (almost) when coming back from Mission Bay. The car came to a stop just as it barely tapped my bumper. I had no damage to my truck or kayak, but the rudder pin left a 12" gouge in the car's hood. Even though there was no damage, this was the main factor in my decision to get the rack.
Thule and Yakima both make nice racks. I use a Thule Xsporter with a home-made kayak rack.
You can find racks at
REI
Rack-It
Track-Racks
The Rack Warehouse
I've also seen racks listed on Craig's List and on some of the kayak fishing message boards.