My assumption is that it will depend on the capablilities of your aftermarket stereo. Does it have some kind of line-in or auxilliary input?
I've also got a Contour (a 1999 SVT) and I added a Blaupunkt stereo to which I was able to add an auxilliary input. There is a wire with a mini, headphone-sized jack that comes out from low on my dashboard and is easy to hook up to my iPod. Sound quality is excellent as everything is hard wired.
If your current stereo doesn't offer the option of aux input, and an FM transmitter is not acceptable, I think it's likely you'll have to look in to getting a different car stereo.
Good luck.
AgFrost