I had this problem. It turned out to be a ground loop between the cig lighter and the stereo via the line input plug. I had to isolate one of the grounds. At the time, my choices were using an isolation transformer on the 2.5m jack (yuck), or using an isolated dc-dc converter for the charger.
I chose the dc-dc converter route. Works great.
I did not try to lift the ground off the 2.5mm plug. That may work also.
Fundamentally, I think that the problem is most portable devices use a small resistance on the ground side of the power input to sense current draw from the charger. When you plug your 2.5mm plug into the same grounded system, it attempts to short out this resistance (diverting some current from the charger through the audio jack), and causes the noise - along with other problems.
I would think that by now there would be a simple commercial solution to this problem, but I have not looked it up, so don't know.
Logically, I would think that you cold also introduce a resistance in the audio ground to solve the problem. Say 1K, or so. That should prevent current draw through the jack. Never tried it. Could work. Typical impedance the audio would normally see from the stereo should be 10K+.
HTH