Exact same problem as many above. I have an Iphone 4 running IOS 4.1 connected to my Pioneer car receiver via the iPod connector, getting random silence / gaps every few seconds. Happens to both normal stored music and Pandora. Even when nothing is playing at all and I turn up the volume, the hiss stops and starts the same way.
Turned off 3g, data networking, all apps, bluetooth, turned the phone off and on, nothing works. Very annoying, makes it totally unusable as an iPod in my car.
Worked great under 4.02, so it seems like a software bug.