You keep referring to only a single use case of iBeacon - retail & shopping. This is the biggest market for beacons and retailers surely will use beacons to gather data. But so does Amazon, and I'd say that more people like Amazon because of offering products they're likely to buy, than hate them because they store their shopping history.
Anyway, there are lots of other uses of beacons. In other cases, no one claims you're getting anything for free. When it comes to dining apps: if they deliver great experience, restaurants will be more likely to use them to keep more clients coming. If Robin's smart office software works well, you will pay them to use it, because they're a SaaS company. If a museum's app makes an exhibition much more entertaining, you'll come back to see the next one. There is no 'hidden fee' anywhere: they use your location data to improve their services. Surely there will be violators, who want to take advantage of this data without offering value in return, but iBeacon is opt-in by design: you need to download the app and give it permission to access your location. What's the chance you will keep using an app that isn't useful and violates your privacy?
Basically, it's a bit like with Uber: yeah, you do share your location. And thanks to that, Uber leverages users' data to adjust fare rates and number of contractors, optimizing their business. But your benefit is clear - you get a great service, much better than huge majority of taxi corporations.
As for advertising: from what I've seen, beacon vendors are pretty visible in AdSense and do a ton of retargeting. We do at Estimote, I've also seen banners from Radius Networks, Kontakt.io, Urban Airship, and at least a couple of others. But I've seen their pages a bajilion times, so that makes me a good target for the ads :) There was also a lot of press about beacons in the last few months, especially with Facebook and Groupon entering the space with their pilots.
Cheers.