It's probably not the NSA — that agency can tap all it wants without the need for bogus towers. The towers were found in July, but the report implied that there may have been more out there.The implicit inference is the military's counterintelligence people operate these towers. Maybe they're looking for spies, maybe for drug dealers and hackers.
The fake towers give themselves away by crushing down the performance of your phone from 4G to 2G while the intercept is taking place. So if you see your phone operating on a slow download signal while you're near a military base ... maybe make that call from somewhere else.
Be realistic, anything entered into any electronic medium - cell or landline phone, Internet, email, texting, photos, data, video, whatever - may be surveilled or hacked. Don't put something out there if you aren't willing to have it examined, possibly by hostile strangers, and used against you. COTTonLINE lives by this rule, we self-censor.