I've had worse than a few swirls and scratches from an automatic car wash before now. I took my (then) brand new Mazda 323F through one once, and the overhead roller brush somehow managed to get under the back wiper.
It snapped the aluminium wiper arm and bounced the blade and the remainder of the arm off the roof with quite considerable force.
So there I was with a brand new car, ready for its first trip to the bodyshop.
I noticed afterwards that some car washes started supplying plastic sleeves to go over your rear wiper arm. From that, I'd conclude that it wasn't an isolated incident.
I tend to wash mine by hand these days, using a huge brush with very soft bristles. It's designed to go onto the end of the hosepipe, but it leaks at just about every joint. I just dunk it in a bucket of soapy water and use the hose to rinse down. It works brilliantly.
All in all, it probably takes less than 10 minutes to wash the car, and you can spend that long queuing for the local car wash (well you could until they bumped the prices up.) I'll only bother with the car wash if the weather's too nasty to be out there hand washing it and the car's absolutely filthy.