What Apple has said with certainty is that it will not be storing the Beacon-collected data for itself. But in an age where data is among the most coveted of possessions, it’s not a huge escalation to imagine that someone will in the very near future.
I think this is the real concern. Not that Apple will collect the data, but that others will — and they will. It would have been great for Apple to have designed the system in a way that doesn’t allow people to collect any data. ((Maybe they have, I don’t know one way or another.))