First, price. Hard boxes cost more.
Second, storage. Hard boxes require storage
Third, some people don't like things that look like photon torpedoes on their cars.*
However...Bags are not as weatherproof as boxes. They're not as aerodynamic and that can cause some gas mile inefficiency.
So now you have all the straight dope. As the knight in the last Raiders of the Lost Ark, "Choose wisely."
*Seriously. Take a good look at some of the photon torpedoes in the old Star Trek movies. Yep.