Einstein:
I've had my S2000 antennae ripped off as well. I really don't use the radio but having the threads in the antennae base showing just doesn't seem right (plus think of all the wind resistance
You mentioned using a rubber plug to seal yours off - any suggestions on where to find the plug?
FYI, I also have an Element so I just swapped that antennae to S2000 since very few people are tall enough to notice!
First, welcome to the EOC forum. I've only been here for a short time myself. You need to update your profile so we know where you are at and what model/year/color E you have.
When you are replying to a specific person, and their original post is from quite some time ago, it's best if you click on their username, and look for all of their posts. The one at the top will be the most recent. I just checked, and Einstein last posted over 3 years ago. I only point that out, because you addressed your question directly to him.
I haven't had my antenna off, but I'm assuming that the threads that are exposed are male threads coming up out of the base? I know you were joking about wind resistance, but I still took from that that there are male threads sticking up out of the base, rather than female threads in the base. My suggestion would be to go to Menards, Lowes, Home Depot, or whatever your favorite mega-hardware store is. In the aisle with the nuts, bolts, and fasteners, look in the drawers that slide out. They usually have the hardened bolts, metric bolts, SS bolts, etc., in these drawers. There are also a few drawers with odd , specialty fasteners and items. Those few drawers are where I think you might find what you need. I think they will have some sort of rubber "cap", or "hood", or whatever you'd call it, that will fit snugly over the exposed threads.
If it is female threads in the base, you can do the same thing by buying a bolt that is threaded on both ends. If you have any old car stereos laying around, look on the back side of them for the support bolt. If it is there, take it out. Most of them are this type of bolt, threaded on both ends, with a rubber cap on them to go in the hole inside your dashboard. If you were lucky enough that the threads were the same as your antenna, you could use that, then put the rubber "boot" (cap, hood....) on it as described before.
I guess it might have been quicker for me to just go out and take my antenna off, then only address the correct scenario!
Hope that helps.