I own a roof mounted rack (yakima) I bought it off ebay used for half the price in the stores
. I chose it for a couple of reasons: 1) I like the way it looks...its like a hat for my car. 2) (more important) if i get into a fender bender, the most common kind of accident, I don't run the risk of losing my bike. Its not covered on most insurance plans
. 3) I too can fitmy bike in my trunk if i lay down my seats but i've found that it is easy when moving the bike in and out to scratch one or both vehicles. On the downside of the roof racks, it has scratched my paint on the tube (mine loads with the tire in place). the rack has also scratched my car but i think i just needed to use a better buffer between the car and the rack. Also I don't like traveling for distances with my bike on the rack, I'm scaed that debris will fly and hit the bike damaging it. It hasn't happened yet.
hope that helps