Both the airlines and the involved law enforcement have a right or even a duty to know who you are when you are boarding the plane. They also have facial recognition data, either from a passport photo or putting a camera in front of the check-in, and arguably they have a right to that.
People walk around with their faces all the time. They post it on social media. Would it be a problem if a security guard lets you through a gate because he recognizes you? Is it more troublesome that all security guards of the airline now can recognize you at the gate?
I think we need to be more precise about what exactly is spooking us and why. Using facial recognition for boarding security is not as big as a problem as facial recognition being used for law enforcement or whatever they do in China now. But that's a topic for legislation and regulation. If companies are prohibited from storing personal data without consent, that should be enough to stop almost any legal infringement.
If such legislation is impossible, because your government is completely unaccountable, or because companies are unaccountable to such laws, then that is a much bigger problem than the potential for violations of privacy...
With regards to privacy I keep coming back to the conclusion that it is more important and effective to improve and enforce regulations than to beat up on particular technologies.