There is a huge difference between a fingerprint scanner for convenient (biometric) access to a consumer device and that required for fingerprint recognition for legal or criminal investigation uses... i.e., multiple digit, entire finger extent imagery with "interesting" topological points indexed for quick comparisons.
In this case, fingerprint recognition is used to check that your finger roughly approximates to the finger that you configured to be allowed to unlock the device. Apple have also specifically stated that the matching parameters are only stored on the device itself and that Apple do not upload it or do anything else with it. While it's quite sensible to have some concern about this being the case or future creep of this information, it's not such a big deal.
Why? This is a consumer device and the matching details will not be unique enough able to match your details on a database of millions of others, instead it's likely to be accurate enough to ensure that something like only 1% of the population could unlock the device because they and your fingerprint profiles are similar enough. Don't forget, this is just about unlocking a consumer device therefore it has to work more often than not compared to real security fingerprint readers where if there's a chance of not being a match they will err on the side of rejecting a match but where if Jo Public's shiny new mobile started doing this depending on the relative temperature, health and water conditions there'd be an uproar that people were locked out of their devices. To mitigate even this, there is always a standard pin number or other fallback unlock method.
I'd have more concerns about it being used to approve AppStore purchases but given that many people don't even bother protect this, therefore allowing their kids to rack up hundreds of $£, etc in in-app purchases, adding a marginally more convenient way to protect such purchase is an improvement.