I have a very similar problem, and it's absolutely driving me NUTS... Let me try and explain my situation, and maybe someone can help?
I just recently got a 2012 SEL Ford Fusion with V6 and the touch-screen navigation system.
MyFordTouch hasn't made it's way to the Fusion... but this option seems pretty nice (and various things like heated seats, I can even get to more quickly since I have physical buttons for those)
I also have an iPhone 4S, and one of the things I was looking forward to the most in getting this new Fusion (my previous car was a Pontiac GrandAm which I loved... but it was 14yrs old and had 197,000mi! I was also sick and tired of needing to tune/re-tune my FM transmitter to get the iPhone audio through my stereo system!!!) was using sync with BT audio to have my music stream WIRELESSLY to the awesome SONY stereo that my Fusion has...it's very nice.
So, what's the problem that's driving me nuts???
Well, when I get in my car... For some reason the stereo defaults to User Device LINE IN, even though I've never connected anything to LINE IN, and always turn off the car with having had audio streaming from iPhone 4S using the BT audio connection... Of course, starting in LINE IN mode causes me to have to hit that button once EVERY SINGLE TIME so that it toggles to BTST!
I've tried to find some option or setting to change the default user input device to BTST (Bluetooth stereo) rather than LINE IN... I just can't seem to do it. If anyone knows how I could possible configure it so that when I start my car the stereo turns on in USER DEVICE with BTST option... I'd love to know, having to click the LINE IN button once EVERY SINGLE TIME so it will then toggle to the desired BTST is getting a little old :(