Even taking into account all the factors you say, it still makes no sense. A modern smartphone is basically a mobile spy device, ready and able to be subverted by organizations such as the NSA to spy on you 24/7. Adding a fingerprint scanner to it is so incredibly minor compared to what they can already do that it boggles the mind why anyone would care about that specific bit.

I'm completely sympathetic to concerns about government spying. I just don't understand why carrying around a mobile spy box all day is fine, but carrying around a mobile spy box that scans your fingerprint is an outrage.