I think the most powerful argument here is that just because one may think that they have nothing to hide, and they don't mind "having their picture taken naked and distributed to their neighbors" doesn't mean that they should enforce their beliefs on others.
That goes both ways. Just because one wants to keep secrets doesn't mean you should stop someone else who wants to know everything.
To make the case for who is wrongly imposing their will, we need need a framework for measuring goodness. The author goes in that direction, talking about measuring the societal benefits of privacy and the systemic harms that privacy protects against.
However, the "secondary use" harm wasn't very compelling. Contract law seems to be the proper way to handle that, rather than privacy.
A better argument was that privacy protects free thought. Unfortunately, he mentioned it too briefly and didn't discuss the conflict of free speech and privacy in enough detail. Perhaps there wasn't enough space, but I think more explanation of how privacy expands "the range of viewpoints being expressed and the degree of freedom with which to engage in political activity." After all, those viewpoints are of little value to society before they are shared widely. One could argue that it's not privacy that is important, but protection against retaliation.
The reverse of keeping secrets (asserting your right to privacy) isn't allowing others full snoop powers (denying your right to privacy), but allowing another to practice full disclosure (asserting their right to freely reveal all).
Playing Devil's Advocate here (I actually agree with you), the main argument against privacy is that it hampers effective and just running of the government. Simply put, the government must gather such information to work in the way that it is told to (we elected almost all of these people, remember). An example of this working properly is search warrants: the government can and will search your private property without your permission, a clear invasion of privacy, but acceptable as it leads to a better justice system. Yes, the government is limited in what it can search, but that power is still held by the government even if the person in question doesn't agree with it.
The question shouldn't be about protecting privacy; it should be about being fair with how the government invades it. For example, the body scanners could be considered not fair as they invade more people's privacy than necessary (or they could be fair if they didn't).
