I have the dock connector option for my factory stereo as well and am also seeing it drain the iPhone battery. What's odd is that it used to charge just fine.
Initially the iPhone wouldn't route audio through the dock connector in my vehicle. It would see that it was plugged in and gave the Airplane Mode prompt, but would only play audio from its internal speaker. It did, however, charge as expected. Then the iPhone software update 1.0.1 came out which solved the audio issue and allowed me to get the audio to my deck properly. I can't say for sure if it was still charging the iPhone at that point, but it definitely wasn't /draining/ it. Then, right around the time of the 1.0.2 update I started to notice significant drops in battery power when unplugging it after a drive to or from work (usually around 25 minutes). The audio still works fine, but the battery seems to drop at least 15-20% over that drive, whether I have any music playing or just have the iPhone idle but plugged in.
So, software problem, maybe? I have a hard time believing something suggendly changed with the dock connector in my vehicle...