I've done it a lot. If you're using a specialty shipper, like Affordable Boat Carriers, you'll need only minimal protection (like a Tyvek canoe cover taped down so it doesn't blow itself apart at 60mph). They take good care of the canoes.
In my experience bad things happen with common carriers. Think about thick bubble-wrap at the least. I've fully crated boats coming back from Hawaii in containers, but never on the mainland. Truck carriers give you mile-high quotes for big crates.
The best source of information would be the builders on our list - they'd certainly have the most experience with shipping fragile boats.