Having been frustrated with this issue and finding no resolution I finally insisted on help from Emich VW in Denver - especially amazing Support from Sabastian from Service and Tyson from sales.
As many of these threads seem to talk past each other, find below my SPECIFIC problem and the resolution. If this is helpful, pass it on.
Hardware:
2012 Volkswagen Jetta TDI
iPhone 4S (running 6.x or all the way up to 7.0.4)
Problem:
You cannot prevent the iPhone from starting Music Player, playing music and streaming bluetooth to the Jetta. If you disable Autoplay on the Jetta stereo, the music doesn't auto play through the car speakers, and you think you solved the problem. But it turns out the music on the phone continues to play and streams bluetooth - causing the iPhone to drain it's battery. Additionally, sound quality on the hands-free system suffers.
Solution:
After 5 hours of work, the key is the LATEST Jetta Software update. Point your VW service person to Technial Service Bullitin (TSB) 91105. The key was to make sure that both the Software Part Number and Software Version number are up to the latest version. I'll state this again as the numbers are subtly different and can easily be missed.
In my example, I had
1K0.035.180.AE
0016
It was upgraded to
1K0.035.180.AF
0008
Notice both changed. Apparently this was surprising.
Enjoy!