These transactions clearing houses sit between the banks and the ATMs. They recieve the card information and transaction requests, then have to connect to the bank's systems to verify the card and the account balances. They also have to be prepared to "stand in" for the bank and approve transactions if their connections to the bank are down. The cost of establishing and maintaining those data newtorks and processing those transactions is charged to the bank, who then has to pass the costs back to the customer. They also have to charge enough to make up for losses due to fraudulent transactions, or "stand in" transactions that were approved, but the customer didn't acutally have sufficient funds.
imagine what the swipe fees are for traveling abroad.
somtimes it costs $20 just to use an ATM!