A beacon in a New York City phone booth ad would need to recognize a corresponding app to push beacon-linked content to that phone.
From what I can see from reading the article this isn't the scary "things that watch you without your knowledge" but more like "things you can connect to if you're nearby" - and given that there's WiFi hotspots and other things in this category too, it doesn't seem all that frightening. In other words you'd have to have allow your phone to connect to them for them to gather any info, and in that case it's not much worse than connecting to a WiFi hotspot setup for marketing purposes (e.g. http://www.washingtonpost.com/blogs/the-switch/wp/2013/10/19... ).
(The fact that the majority of people leave their phones in a "promiscuous" mode with all the radios enabled and constantly looking for things to connect to, and submissively install apps without reading their privacy policies/terms of use carefully, is a different although related issue - but this is something you can educate yourself and protect against.)