I am able to use my iPhone 4 with iOS 6 in my car. I have a 2011 Honda Accord EX-L sedan with the navigation package and connect via a USB port. I use Bluetooth only for the telephone function. Here is what how I use the device in the car and what I have learned:
I use my iPhone to listen to podcasts and audiobooks more than music. Often, I listen while at work and go directly into my car, plug in the phone, press the AUX button and continue the podcast I had been listening to through headphones. Prior to the addtion of the Podcasts app, this worked flawlessly. Now recall that iOS 5.1.1 had the Podcast app and still allowed podcasts in the Music app. While still in 5.1.1, if I was listening to a podcast through the Music app, it worked perfectly when I plugged into the car. If the 'cast was through the Podcast app and I plugged in, I would get a few seconds of the 'cast and it would cut off and the NAVI screen would read "Not Supported."
Now, with iOS 6, podcasts are restricted to the separate app. No more in the Music app. Anytime I plug into the car when the last action I did was listen to a podcast, I get "Not supported." The Podcast app cannot communicate with my Honda. So, my workaround is this: Before plugging into the car, I make certain the last thing I listen to is something from the Music app. Once plugged in, I press AUX. The music starts, I bring up my iPod menu, select Artists, and find the podcast on the Artists list and select it. It works everytime. Not ideal, but no need to perform System Restore or reload my music. I believe there is an issue with the Podcast app, at least with Honda.