Some roof carriers/baskets have brackets available specifically for carrying jerry cans. Obviously the less weight on the roof the better, but I figure a slightly higher center of gravity is a hell of a lot safer than carrying fuel inside a vehicle. Just check the load rating of the carrier & your vehicles roof first, and remember that rating is probably for smooth on-road conditions, so don't load too close to that limit.

Also, it's easy to chuck a tarp over the whole roof load to conceal it.