Strawman argument. The article comes off with a mild 'so what its no big deal' tone.
The fact that they crack crypto is not the controversy. The controversy is the mass data collection that dragnets everyone. The other controversy, among many, is that they are paying businesses for back doors to their supposedly secure encryption. We are supposed to be innocent until proven guilty. We are supposed to not be searched and seized without due cause. It's a human rights concern.
anyone with access to that research can—at least some of the time—crack VPNs, they can crack HTTPS, they can extract data from iPhones.
So what. They are doing it on a more massive scale than anyone else. Orders of magnitude more. History has shown that government is not to be trusted with this degree of power.