You could wire it up to power on only when Bluetooth is on; I believe another board member is selling a little doohickey designed to switch 5-volt devices with Bluetooth and you could adapt it. Or even hijack the keyboard signals to toggle power -- I did this when I added a ThinkLight-type LED to my A90.
Another thought is that you could use a switching DC/DC converter like the PTN04050C to step 5 volts up to 12. The noise of the switching converter might adversely affect the transmitter, though.
Ooh, I just had another idea too -- put an A2DP receiver in your car, wired directly the stereo. Then you'd just use the netbook's built-in Bluetooth hardware and you'd also have the clarity of digital transmission.