I've got a '98 Wrangler, soft top, and had the same problem. I also had a problem in that I did not want to drill any holes in the car or bumper. I made a dual band j-pole antenna out of tv twin lead (there are many websites about how to make this antenna). I housed it with 3/4" PVC pipe, the whole length of the tv twin lead (about 5 feet or more). I hung the antenna by drilling two small holes into a PVC cap, then hung the antenna with some string through those holes, and put the cap on the top of the PVC tube. At the bottom of the pole, I drilled a hole in the side where the antenna ended and coax began, and fed the coax out of the PVC housing tube. I found a flag holder, for a flag that might hang on a pole on the side of a house. The angle of the holder could be changed, and I made it point straight up. I secured the pole holder onto my back bumper with the help of two bungee cords wrapped around it--no drilling holes. I just put the PVC tube in the flagpole holder, and fed the coax into the car above the upper right corner of the trunk, though a nook in the canvas top--there is no stress or pinching of the coax. It's a great antenna, and it works very well.
These instructions are not incredibly clear, but if you are interested, email me at KD5ZZU@yahoo.com
and I will be glad to give more detailed info and some pictures of my car.