The iBeacon transmitter may be passive, but the signal is typically passed to an app running on a phone, which can do anything, including post all it's position and time info to a server online.
The good news is that it appears to be opt-in. In most, if not all, instances a user needs to install an app and enable location services before the iBeacon will trigger anything. No app listening for a particular beacon or set of beacons, no problem.
Of course, there could also be malicious code running on the phone, installed by the government or spies, that could silently record everything. That could work now with gps, voice and video recording, wifi network positioning, etc. iBeacon is just one more set of data to collect.
You could in theory set up a Bluetooth surveillance network though couldn't you? I really doubt that's remotely the goal for Apple but Bluetooth always on would make it possible I think.
It'd be quite a lot easier to do this with wifi, and indeed such systems exist, for monitoring people in shops etc. iOS 8 makes it substantially harder for these to work effectively (through randomised MAC addresses when looking for networks), which seems like an indication that Apple isn't interested in facilitating this sort of thing.
