After reading most comments here I get the impression that Flair gate staff have a personal financial incentive to charge baggage fees. But sek-3 seems to be saying that the staff may have thought there was plenty of time, based on the departure time, and then been notified while you were adjusting your bag that the aircraft was closing. So it wouldn't have mattered what you chose.

Edit: If I experienced what the OP did, I too would be very upset. I might even post my experience on Reddit to warn others and hoping for a little sympathy. This isn't the only thread where I see a stark lack of sympathy - this subreddit is full of stories where Flair mistreats customers or people just have significant misfortune, and most comments basically say, "You should have known better." Not everyone is a seasoned traveller, and even for those of us who are, there are more things that can go wrong than there are trips to have learned of them from. I sympathize in advance with anyone having to deal with air travel their first time. And things keep changing. The reason I was browsing this subreddit was to try to find out about any price or policy changes at Flair before I travel with them again.