unless you're about 6' tall, or you drive a F1 race car that's nice and low, a roof rack is basically a terrible idea. They also do hurt your fuel economy more than trunk racks, and keeps you from going through drive-thrus, parking garages, low bridges, etc.

trunk rack is the way to go. hitch or strap on doesn't matter - whatever works best for your car.
sure it can keep you from getting into the trunk, but that's only when you're taking them on long rides. short trips you don't need to get into the trunk, do you? don't forget you can always get to things through the back seat into the trunk as well.