The small storage compartment in the back of my 2007 2-door jeep wrangler Rubicon is wet, soaked with water. Where is it coming from?

Water inside a jeep? Welcome to the club.
The fact that it is down near the Jack storage makes me think one of the drain plugs worked it's way loose.
Next check your soft top is closed properly and all of the plastic fins are wrapped tight into the steel body. Getting the rear soft window panels hung, start the zipper but not all the way, wrap the fins into the body, the wrap the fins into the door-frames, then finish the zippers and Velcro.
Any other method results in plastic side windows acting like a funnel instead of an umbrella over your jeep.
If it's a hard-top check you gaskets are intact and seated properly. I have both tops and the hardtop leaks worse.
Damp-rid, or hang an incandescent work light inside the jeep overnight, should dry it out.
After about 10-15 days of wet carpet you will smell the 'funk' starting to grow.
Good luck, and have fun out there.

If your Jeep has a soft top -

I have a 2007 Unlimited and has the same problem. My Jeep is a soft top and the water came from the rain and a poor seal of the back window. Part of the problem came from the displacement of the plastic "c" shaped "rear window bar holder" that clips on to the rear on either side of rear window. Ocasionally the clip pops out of place and breaks the seal between the rubber on the window and the rear sides of the Jeep.