I don't understand all the hate on roof racks. How many times have you actually driven into a garage with the bikes? I've gone under drive thrus a bunch of times with bikes and they typically have enough clearance (granted I drive a Civic, they're very small).
Roof racks were seriously one of the best investments I made. They're always on, so you don't have to set up a rack to carry a bike; just takes 30 seconds of securing it on the roof. I also have Thule Big Mouths, which means I don't have to take off the front wheels. The bikes are extremely secure and sturdy on the roof. Plus it's a LOT more hassle trying to steal bikes off a roof rack compared to off a trunk rack, in which you could probably cut it off the car.
Not to mention how awesome a car looks with bikes on the roof