How can I fix the "pops, cracks and hissing" sounds from iPhone audio played on Ford Sync over USB?
I read a post about this before on the apple discussions board.  The upshot of it is there doesn't seem to be a permanent fix.  However, people have provided several workarounds of which some work for some people but none seem to work for everyone.  Here's a few things to try.  


Leave iPhone in Airplane mode while connected  
Turn off WiFi on the iPhone
Turn off 3G on the iPhone
Connect the cable while the device and stereo are off, then turn both on
Rebooting the iPhone  


I can't say from personal experience whether any of these actually work but anecdotal evidence from peoples experience in the thread linked to above would suggest they may.  I think it may be a hardware design issue that is probably due to interference from the USB cable when it's connected but many people on that thread say that it only started when they updated their iPhone 4 to iOS 4.1.  If you're on that version you could try updating to the latest version of the iOS software.  You could also wait until Apple release iOS 5 which is likely to be October 4th 2011 as they may have fixed it.