Roof rack or trailer
From KayakWiki
When moving longer distances, moving the kayak with a vehicle is convenient. Roof racks are an obvious choice. Another way to transport the kayak by vehicle, is to build or buy a kayak trailer.
The choice of rack or trailer is an interesting one. With the price of complete roof racks from the big companies going through the roof, a trailer is not necessarily a significantly more expensive proposition, especially if you are moving several paddlers around. Roof racks put the kayaks up high - especially if you drive a truck. That can make loading and unloading a pain. With the kayaks on the roof, aerodynamic drag is somewhat higher and fuel economy suffers. It's not unusual to see 20% or more increases in fuel consumption. Trailers, by riding in the vehicle's slipstream, do increase drag but by a lesser degree. With today's fuel prices, you can save a lot of money on fuel with a trailer. That might not make up the price difference between a rack and a trailer, but it can come close for some.
Trailers do suffer in other ways. They increase the length of your vehicle and you have to learn how to handle parking and backing up with a trailer. As well, you will incur higher costs on some ferries and toll highways or bridges. At home, you need to have space to store the trailer when not in use. There may be licensing costs as well. Finding appropriate parking at the put in can be a pain too.
With a roof rack, you are limited to the design load for the combination of rack and vehicle that you have. In some cases, that is not strong enough for two sea kayaks. As well, all your gear is going into the vehicle - some gear could go into the kayak on the rack, but only to the load limit of the rack. Some trailers, on the other hand, can carry four sea kayaks comfortably and have a box on the bottom to carry some, if not all, of your gear. As such, four sea kayakers with all gear can fit into a minivan or mid-sized car with a trailer. Commercially available roof racks realistically limit you to two sea kayakers at most.

