The author, perhaps, isn't bothered by the many reasons why other people unlike himself want privacy and have wanted privacy throughout history. Maybe the plight of others will never be good enough for him to change his advocacy. There's irony in his case. Not so long ago, and to this day in many parts of the world, revealing oneself as an atheist would have made one subject to extreme persecution, if not quicker death. It was through a long course of secrecy, over a gradual shift in public perception, which was rapidly accelerated by the soft veil of the internet, that more people began to feel safe enough to 'come out' as atheists. (Granted, that history didn't have a complete lack of privacy. Yet, if it had, I'd wager that the world today would have even fewer "heretics" upon whose shoulders others may rest their unpopular thoughts.)
Transparency should be a growing expectation people have toward all governments and institutions that wage force over people. I agree with that part.