I sent in my last payment on my MBNA loan (central air system replacement) today. Completely painless and got a lower rate ... once I told them I was shopping around ... which was shitty, but not painful. I think I liked the experience because I submitted the request online, got a call in 15 minutes, and picked up the loan check an hour later. That's what I call speedy! Also never had a problem with them spamming me with junk mail in either snail or electronic format, so I know they didn't sell my info. The customer rep. who answered the phone so I could get a payoff amount was also quite helpful ... and a slight bit flaming ... which was kind of amusing. :)
Most of those fees are there to prevent people from using those payment methods all the time and to encourage people paying on time by sending in the payment before the day it's due. The other side of the coin is that the bank may be charged a fee to perform this service themselves, so they charge the customer the fee on an as-needed basis instead of offering it free and recouping the costs by charging you to have a checking account with them. They also have to pay the people to maintain the computer that runs the phone system and pay the people who take your calls.