Shuffle is not recognized thru 2013 Santa Fe usb port. Any suggestions?

You should consult the documentation or tech support for the car audio system, to see if a shuffle is supported as a device connected to the USB port. Also, there may be a setting on the car audio system, where you tell it that you are connecting an iPod to the USB port, and not something generic like a USB flash drive with song files.

When you connect an iPod to a USB port on a car audio system, it is just acting as a storage device. The car audio system is reading song files off the iPod and doing all the playing. Therefore, you may want to use a cheap USB flash drive with song files for this purpose, instead of an iPod. Here's one that barely sticks out of the USB port

http://eshop.macsales.com/item/SanDisk/SDCZ33008G/

and has four times more storage compared to a 2GB shuffle. You can also leave it connected to the car audio system, except when you want to update its songs, instead of having to constantly connect and remove an iPod. If you forget your iPod in your car, extreme heat or cold can cause damage.