I don't do anything special, except put my bike in, rear wheel first, derailleur side up. My bike is really light.
I used to have a small sedan where I put the seats down and slid the bike in the back, through the hatch. No taking wheels off, or anything. My bike is small, though. No cover on the car or the bike and frankly, I didn't care if a little grease got on the upholstery. Sometimes, I had to work a little to get the bars in the right position to get in there. Now I have a station wagon, with black insides, so the grease part is a moot point. My second bike, with the couplers is a bit heavier, mostly because of the rack on the back, so it feels awkward to put in the car, but it's not hard.
On Mondays, I sometimes ride with my last client, who lives about 5 miles from me. So, I end up with my bike in the back all day, as I don't have time to go home first. Every other week, the person I see before him lives in the projects in Lawrence, and I never once have worried about my bike. Maybe I'm naive, but, you can barely see inside the car, and the bike is kind of in there, in between all my therapy "toys."
I used to be more worried about my car, but then i saw that an Audi didn't really stand out, as a good portion of the drivers are using the profits of the drug trade to drive really nice cars.