I just registered my daughter for her club soccer team for next fall. I opted to pay online and after I hit the "submit" button for the payment a window popped up saying that I was going to be assessed a $1.75 "convenience fee" for paying online with a credit card. A friend of mine had a much more appropriate term for this kind of fee; he called it a d-ck fee. And if you're wondering what the dash stands for let's just say that the word would not be a bird that quacks.
That kind of crap makes me want to drive over to the office and pay with a sack of pennies.
Befuddled 
I dislike not being told about such a fee in advance, but don’t mind the idea of a convenience fee. After all, I’d much rather pay an extra buck or two to pay online and get it over with than to have to go to the trouble of writing and mailing a check. I’m so lazy! But really, especially with non-profits, I don’t mind the convenience fee because I know it helps them cover the cost of using a merchant account. For-profit businesses, however, should suck it up. And all of those should warn us ahead of time!
First off, I agree that it needs to be disclosed up front. I wish it had simply been on their payment form rather than on a pop up window that appeared after I put in my info. I still could have cancelled it out, but it was just a nasty little surprise.
I also see what youre saying re. the fee covering non-profits CC transaction fees, but my viewpoint has always been that they should just include the fee (however much it is) in the price and then I dont have to even think about it. If you think about it, its just as convenient for the non-profit to be paid by credit card as it is for us to pay them with one. They dont have to process the check when it comes in and they dont have to wait the extra time to get their money. It may not seem fair to make people who pay by check subsidize the credit card payers by having the fee included in their price, but when you get right down to it all pricing includes some cost that isnt directly impacted by every customer. For instance the Y builds in the cost of maintaining the pool to my membership fee, but I never use it.
Truly, though, this is just one of my pet peeves. It didnt stop me from paying by credit card, because I sure as heck wasnt writing a check and sticking it in the mail, but it sure did give me a bitter taste in my mouth.