Since fingerprints can't be changed, he more widely they are used for authentication, the more likely that they will be compromised and the less useful they are for authentication.
However, it's not at all an argument against using fingerprint scanners as an optional choice for authentication, just because the scanner could be used to steal your fingerprint.
Fingerprint theft is a problem regardless. You can't really target systems that enable that theft, because it's an ever-present risk. Instead, worry about systems which fail due to such theft.
Fingerprints are fine for a gym, because who cares if somebody fakes yours. They're fine for a smartphone for many people, because it's intended to stop casual theft, not be an impenetrable barrier. Fingerprints should definitely not be used (at least on their own) for, say, nuclear launch authorizations or other things of similar import, because they can be stolen and faked.