The main difference between beacons and RFID is the range. RFID only works up to 1m while beacons typically reach 50m to 100m, even more for specialist beacons. It’s also possible to get an indication of distance to the beacon whereas with RFID it’s just ‘seen’ or ‘not seen’.
RFID tags are less expensive than beacons. However, as the range of beacons is much larger, fewer readers are required thus compensating for the extra cost. It’s also possible to totally cover a much larger area.