Nothing really new in that article. The map indicates where "towers" were found by the CryptoPhone. It doesn't say that the physical towers are located there (hard to word this so it makes sense). Each one of those pins could be a location where a backpack sized box was placed on top of the tallest building in the area. No FCC or FAA violations. If you watch the video @blowdart posted you'll see this demonstrated with a rig that is 100% legal (so the presenter claims) so long as the operator has a HAM radio license.
I'm not claiming any of this is good and that we shouldn't be concerned and investigating. But the idea that somehow giant towers have been erected just so the government can spy on us sounds like a massive over reach based only on what we do know.
There's towers and there's "towers". :)