My Nexus 9 with M more or less works, but the Bluetooth pairing doesn't seem to work (and the HU popups make it unusable); it looks like it can't handle a PIN or whatever.
I installed the updated Android Auto on my nexus 6 on M and after I changed the USB connection to MTP I was able to get it connected but when I try to play music the UI constantly reloads but music does play through.
The update I received was from the Google Play Store, dated 6/3/2015. Not sure why Google Play Store doesn't just have the latest version up all the time, especially for an app that doesn't "hide" like Google Play Services does.