There are many differences in iBeacons and Physical Web beacons but it really boils down to intention. Beacons configured as iBeacons typically work with only a single app so that every iBeacon app has it own associated fleet of beacons or the deployer has bought into a beacon network. iBeacons broadcast a number called a UUID/Major/Minor and exist in a siloed system meaning the user must have downloaded the correct iBeacon-enabled app, have enabled bluetooth on their device, have enabled and allowed location services access for the app, and have opted into push notifications from the app. iBeacons we're designed to only work with iOS devices but there are libraries to bring it over to Android devices as well.
Alternately, Physical Web beacons are universal and work with any compatible Physical Web scanner/browser, including browsers like Chrome, Opera, and Firefox OS as well as any other compatible apps. This essentially means that anyone with any Physical Web browser has the ability to discover your Physical Web content, not just those people who have downloaded your app.
The Physical Web is a vehicle to facilitate people in discovering content around them on their own terms while iBeacon is more about custom app development, pushing notifications and tracking users.This can be summed up by the nature of the two code bases... the Physical Web is based on the open-source Eddystone beacon protocol, while iBeacon is Apple’s proprietary protocol.