@4thtwin,
I can understand certain fees. It honestly is hard for me to tell if what you are quoting are unusually high fees or not without really knowing what is going.
Basically if this is a smaller outfit, they may be paying a company to process these fees. A landlord is not in the business of having a payment system and it would be costly for them to have someone come in and set up their own processing system. Most of the smaller outfits have a company take care of this so it costs them money. Even my town to pay say my water bill charges me a fee to pay online. Why? Because the town using someone else for all this processing and it costs them money.
Another thing that places charge more fees for is if you use a credit card. Why? Because each credit card transaction that you make - the business receiving that payment must pay a fee to the credit card company.
Now what about small businesses that don't charge a fee - why can they do it? Well simply they increase their prices to compensate for these fees. So you end up paying for it one way or another.
I know the place I go to get my nails done - they will take a credit card (without additional fees) but they do ask if you pay by check or cash as it keeps their costs down. I usually am prepared and pay cash to help them out - also I like their lower prices so I try to accommodate them.
Now that is not to say - that some places may take advantage of this by making the fees even higher -- you could always ask them why the fee is so high? Maybe it is because of years of giving it to you for free they are trying to catch up.