I can't speak from personal use but it seems like it would work fine. I assume you are talking about the new iPod with the multi touch screen but it looks like it will plug right in the bottom, I went on Apple.com and looked at pictures of the new 6G iPod and it looks like both the proprietary port and the headphone jack are in the same location. Hope this helps.
I have a 2010 elantra -- probably has the same stereo system as the sonata. I just got an ipod nano 6g as a gift. It'll play songs fine, but there seems to be a display issue: songs are displayed on the stereo display alphabetically according to the file name assigned to them by the ipod (so it'll be something like AS07.mp3 and B2S3.mp3 etc). Once the song is selected, you can view info about that song (artist, song title...) but you cannot browse songs by title/artist/album, and the songs are organized in no logical order on the ipod itself (Apple's way of ensuring users use iTunes). Best I have been able to do is set it on shuffle (otherwise it'll play in the same order every time you plug it in, starting from the first file name alphabetically).
So the 6g will play, but you can't expect more than a shuffle playlist which includes all songs on the ipod.
If anyone has been able to get around that, let me know!
Hope I've been helpful.