I knew a guy that refused to have his fingerprints scanned for a timeclock because he had done some, um, less than "legal" things in the past and was concerned that somehow his prints might end up connecting the dots.
I can TOTALLY see criminals and/or people with tinfoil hats being terrified of the Touch ID. Given Apple's history of protecting our privacy and the boundless love of the Patriot Act, if I had committed a crime in the past and had not been caught I sure as heck wouldn't...
All boils down to how paranoid you are, but if prison and a 300lb man named Sindy cuddling you at night are involved I can sorta get the concern.
It's not about someone LOOKING to get your prints. If they knew where to look, they'd be easy enough to get (doorknob, car door, etc.). It's the "A-Ha", "Gotcha!" moments the criminals are trying to avoid that make the Touch ID oh so fun!
Bottom line: If you have a valid reason to hide your prints, do you trust Apple to safeguard that, especially when the NSA comes and says "hey Apple, we hear you got a nice database of fingerprints with no presumption of privacy there... mind if we take a look?"
But ya, I'm sure they don't keep that data... ask Snowden