iBeacon helps your phone find itself and thus you. It doesn't let others map your phone.
A merchant could make a system which finds you using iBeacon by self reporting. That is your phone finds itself and then an app on your phone tells the merchant. So if you want to find yourself, you can using iBeacon. If you don't want to, you don't. If you want the retailer to know where you are, you run their app which reports your location using iBeacon. If you don't want to, you don't.
The other kinds of systems which track your WiFi signal around the store, where you are tracked without opting in, those are more likely to create privacy issues. Target already uses these kinds of systems.