1. Lack of clarity. I've no problems paying a fee I want and use. But when the fees are hidden at point of sale, and then added later it makes comparisons hard or fees I don't want getting added because I didn't know about them in advance so couldn't change behaviour to avoid them.
2. Fees that don't accurately capture the benefit Vs the cost, and are gamed. Things like "2 peices of hand luggage" with no weight specified. I once had an attendant tell my wife her hat she was carrying counted as one peice, so she had to put in her bag to walk past the check-in desk to avoid being charged a fee for extra hand luggage. And then you get the opposite with schemes like wearing vests to carry extra items without it counting in your hand luggage allowance. I once had to move ~2kg from my hold luggage to my hand luggage because one was over and the other under. Why not literally charge a per kg fee regardless where you store it that way everyone pays for exactly what they use, no gaming. The current fee structure tends to incentivise maxing out on hand luggage to avoid hold fees, which means overhead storage gets crammed full. Charging per kg would shift a portion of this to the hold and make the cabin less cramped and better for everyone.