Well, tin-foil-hattery traditionally refers not only to the paranoia associated with the probability of being watched but also with the malicious or manipulative intent of those people or groups. Schneier needs to protect himself from the possibility of either his data being used in a manner to prosecute or punish or action taken to stifle work he has so far kept private. It's more than reasonable for him to give credence to the threat of a self-interested government agency acting maliciously toward him.

However, Schneier was a target well before this due to the nature of his work. It is exactly the scope of the recent revelations that throws the conventional thinking on where the fuzzy line between an appropriate risk assessment based on position of interest and the general population. When the potential dragnet is widespread and permanent I no longer have to only consider how important I am now (which I'm not), but I also have to consider if I will ever be take on a role that IS important not just now, but then.