When I first got my roof rack I was constantly watching through the sunroof to make sure I did not loose my Trek. Since then I have taken my Trek and my wife's Canondale to Custer State Park and Breckenridge. Each trip was nearly 1000 miles. No problems whatsoever.
The roof and hitch mounts each have their pros and cons. The hitch mount is easy to load and will accomodate kid's bikes and the touring bike that my wife wants (anyone looking for a pristine Cannondale F400?).
The roof rack allows more options for carrying loads such as lumber, bikes, boards, cargo boxes, etc.. Or even two 3/4" sheets of mdf for your little brother's subwoofer project...