My car is just big enough to put my bike inside, a Subaru Forester.
My buddys' bikes have to deal with the bugs associated with a roof rack.
I wouldn't have it any other way.
It might be an old wives tale or something that ceased to be a problem a decade or more ago, but the only bad things I've heard about transporting bikes on a roof rack is the 75mph wind can literally blow some grease out of or at least towards the back of a cheap POS loose ball headset. Apart from that, the biggest problem is forgetting about the bikes when you pull into the garage. That's another reason my bike goes inside.