The debate here is about a new policy of some tech companies, Apple included, that encrypt data in such a way that the decryptions key are only stored locally on user’s devices. Entities like the NSA cannot simply subpoena Apple’s servers to get at data stored in this way, because the unlock codes are in the possession of the user, not on Apple’s servers.
Obviously, governments hate this. This means collecting evidence for things like terrorist plots is now much, much harder and politicians are starting to push back against this type of security.
Personally, I tend to agree with Cook. Apple should not be prevented from offering this level of privacy, simply to enable institutions to detect criminal activity made by a minority of the user base. Threats of terrorism cannot hold back technological development that has far-reaching benefits to society.
That being said, I think Cook will relax this stance, to some degree, in the future. There will come a time when Apple wants to release new products and features that rely on personal data analysis. When this happens, I expect Apple to make everything explicitly opt-in to remain consistent PR-wise.