There are all sorts of reasons fingerprints are not a highly secure authentication mechanism. Just as there are all sorts of reasons passwords and other techniques are imperfect. Password entry can be observed. Chosen passwords are frequently insecure, particularly on smartphones where brevity is so important.

Fingerprints are an excellent mechanism for almost all threat vectors for your average consumer smartphone. Your friends, enemies, and criminals would have to go through enormous, expensive, and clearly unethical efforts to access your phone. Given the convenience and security of this, I'm entirely happy with the security of my thumbprint-encrypted iPhone.

It's important for people who are dissidents or engaging in criminal activity to be aware that their brain is more secure than their fingerprint, although that seems entirely obvious to anyone capable of maintaining a high security lifestyle.