My iPhone 3GS (iOS 6) has started playing out of the left speaker only on my car stereo. Before the new software release, it was playing out of both speakers. When I switch to radio mode on my car hi fi, it will play from both speakers so it appears to be an iPhone problem rather than a problem with my car hi fi.
iOS 6 has a new setting to mix the sound. I would check there first, and then see about other sources to see if it's particular to how you are routing the sound to the car (cable or bluetooth).
Hopefully, it's a software setting that got set on you as that's the easiest thing to correct.