I've also got similar problems with an AVIC 5000. Up until last night I had an iPhone 6. It is a roll of the dice as to music making it out through the AVIC. I just upgraded to an iPhone 6s on 9.2 and the problem is worse. I'm feeling like this is mostly an Apple issue because It appears that audio from Siri and other apps will work, it's Apple Music that is the problem. No sound. The playback progress counts away. Sometimes I will hear a super loud digital buzzing sound until I unplug the phone.
Sometimes a reboot fixes all of this, sometimes not. It's honestly bad enough that if I could