Could be lots of things -- worn tires, defective tires, tires with uneven wear pattern due to poor alignment, bent wheel(s), worn slip joint(s) on either driveshaft (or both), bent rear axle flange, etc., etc. You said you "feel a subtle vibration," but it's not in the steering wheel -- where do you feel it (seat, feet, etc.)? Is there any associated noise? Is the frequency of the vibration consistent or does it rise and fall with speed changes? Also, what are you used to driving? What kind of tires does your Jeep have on it right now? Have you ever driven any other vehicle with those tires, or similar tires. Can you tell if the Jeep you bought has been wheeled hard (scars on skid plates, control arms, rocker panels, scratched wheels, etc.)? There are probably a million other questions to ask, but these will make a good start.
If you're a new Jeep owner, and from what you said it sounds like you probably are, one thing you need to know is that your JK is probably never
going to really be smooth. It may be "smooth for a Jeep," but that's about as good as it's going to get. Aggressive tires all by themselves, can create vibrations that you'll never feel in a vehicle without those tires. Vibrations, to a degree, are just the nature of this beast.
It's hard to know from the information you've given if you have a problem brewing, or just don't know what to expect from your Jeep because of inexperience. More info will help us give you some direction, but in the mean time, crawl under your Jeep and see if you can move the driveshafts up and down. I'm not talking about rotational motion, but as if you're trying to bend the driveshaft into the shape of a bow. If you have that kind of play, you MAY have found your issue. Also look at your tires and see if they're worn in a pattern that's not smooth and flat across the tread blocks. Check them for bulges on the sidewalls (which I would hope your tire shop would have found when they balanced them). Have someone drive behind you and see if any of the wheels appear to be out of true. These things can be a long, drawn out process of elimination, and you still may not resolve it until it becomes bad enough to easily identify. And again, that's assuming you really do have a problem to start with instead of just being unfamiliar with the nature of the machine.
Hope this helps get you started. You should also go make an introduction of yourself in the Welcome thread. And you'll find that if you give evidence in your posts that you have searched out a problem by reading some of the other posts on the forum, the community here will be much more helpful than otherwise. Welcome to JKO and to the world of Jeeps. You'll probably be hooked like the rest of us, so just get ready to start spending money on it.