The fingerprint scanner is not intended to protect your personal data from being accessed by nefarious cyber-spooks or crackers. The $5 dollar wrench technique is fairly effective in bypassing such security anyway.
The fingerprint scanner is there so that when your phone is nicked by a mugger, they can't reset to factory defaults and sell it on eBay. If some knife wielding thug that robs me of my phone has the intellectual capability of lifting my fingerprints off the case and then using them to bypass the security, he still has to know my AppleID password before he can remove the 'Find my Phone' feature.
Give Apple a break. This is just another layer of security. It's _not_ the panacea to all our security woes, and they have never claimed it was.