Don't take the bait
I think they're trying to ferret out bad attitudes and/or are searching for inconsistent question responses.
Reiterate how grateful you are about getting an interview - airline interviews don't grow on trees, you know - how much you enjoyed meeting everyone, how excited you are about the notion of joining Lousy Commuter Airlines, etc. Don't comment about the fairness of the interview, except to say that you appreciated being given the opportunity to present your qualifications in person. You could say the process afforded you that opportunity and that all you've wanted was to have that opportunity, i.e. your day in court.
Above all, don't opine on any changes you would make to the company. You're just a visitor. It's not your place to comment, but don't say that it's not your place to comment. Put a happy face on it. Just say that you're impressed by the professionalism exhibited to you and you would be proud to be a pilot for Lousy Commuter, etc. Hit some specific points that impressed you.
Don't forget to reduce these points to writing in the thank-you letters you should send to the people you met at the company; letters you should write and send the moment you walk through your door at home.
Hope that helps. Good luck with your interview.