When you put your key into the car and crank it up, the stereo comes on as the key passes the accessory position (ACC), then blinks off for a second as the car attempts to start. Once the engine is running, the stereo powers back on and resumes operation. If you're the kind of person who turns the key quickly, this process (On-Off-then On again) could happen a second or two.
Here's what it sounds like is happening to your iPod: During that first blink of power to the stereo, the system sees and attempts to connect to the iPod. The iPod goes into connection mode like it's programmed to do, but before the process can complete, your car stereo has already rebooted. Sometimes, if the timing is right (or wrong, in this case), this leaves the iPod confused. It's ready to connect, but there's no host to connect to. When you manually disconnect the iPod and reconnect it, the connection process is able start over and finish successfully.
The next time you crank up your car, watch your iPod and you may see it spring to life and make that "d-d-dun" noise just before your car cranks. There's nothing wrong with your iPod or your stereo, it's just a slight timing issue.
Your options are a) disconnect your iPod after each use and reconnect when you get in the car, b) stop for a moment at the ACC position when cranking your car to give the iPod a chance connect-disconnect-reconnect, c) or just keep doing what you're doing knowing that you're not really going to break anything. It's a minor inconvenience, but I'd recommend option C.