As a new Jeeper (traded in 1994 Mustang Convertible that I loved for 16 years), I too was worried about frying my stereo if caught out in a rainstorm. To allay my fears, I looked for a Marine stereo with the thinking that if it's good enough for a boat, it should be just fine in a Colorado downpour or two.
I found a Kenwood KMR-440U CD receiver w/USB & Aux interfaces/jacks on the front. It has a removable faceplate to discourage theft and it even interfaces with and controls iPods & USB devices through the stereo itself. I haven't yet installed it as the vendor sent me the install kit for 07 & up instead of the kit for my '06 TJL, but expect to have it installed w/in the next 2 weeks & can't wait to jam to my own playlist already!
Hope this helps answer your query...
Here's the URL to the KenwoodUSA.com details:
Kenwood - KMR-440U
The KMR-440U is an Advanced Marine CD Receiver Featuring:
• Marine Wired Remote Control Ready for KCA-RC60MRW and KCA-RC107MR
• Full Dot FL Display that is Selectable Between 2 Line or Large Text
• Front USB and AUX Port with Sliding Cover
• USB 1-Wire Direct Connect for High-speed Control of iPod/iPhone Audio
• Direct Search Function for iPod
• Illuminated Front USB and AUX Port with Sliding Cover
• New Enter and Return Key Operation
• Favorite Function Presets
• My Playlist Function for iPod
• MP3/WMA Playback
• 3 2V Preamp Outputs