Iphone Connection Through Car Stereo?

Right, i have my iphone connected to my car stereo via usb.

Everything works fine like playing music and when i get a call the music cuts out for the phone call but when i answer the phone call it doesn't come through my speakers.

Why is this?

Look in the settings of the car you might need to turn the call settings to play out of stereo.

This happens because no doubt your stereo is not a phone kit, the usb socket was originally designed for playing music from a usb memory stick, so when you plug your iphone in, your stereo reads the iphones hard drive as a usb stick. When a call comes in, and your music mutes, that is the iphone doing that, just as it would in normal operation, not the stereo. And the sound from your iphone is then not coming from the hard drive of the iphone.
if you want your calls to come throught the speakers like your music, then go and get fitted a parrot mki9200