I've never used a roof rack for my kayak, but I imagine it would get old quick. You should look at the "Post your trailer" thread at Texaskayakfisherman.com. There are some great DIY builds there. A lot of guys modify a boat trailer, and a lot buy a trailer from Harbor Freight and modify it. This would save you big bucks over the Malone kayak trailers. I'm thinking about buying the Harbor Freight 4' X 8' trailer to modify for kayaks.
Towing a trailer is all about practice and common sense really. The biggest difference when towing is turning corners. You have to allow more room so the trailer tires don't hit the curb.