Very disappointed ☹️

I recently took a flight from Cape Town to Bloemfontein and upon checking in, my bag was overweight and I was sent to the payment counter to pay for 1kg extra, yes one kilogram. Upon boarding the plane, I noticed it was not a full flight at all. In my row alone, 4 out of the 6 seats were unoccupied. Now I understand rules are rules and I understand the cost involved regarding extra weight, but where is the discretion?