It's basically a way of hiding some of the cost, to make the service or product look less expensive than it really is. It's not so very different from the airline that quotes a fare to get you from A to B, and then adds a check-in charge, a baggage charge, and so forth.
There's no logical reason for it. After all, you don't expect to pay a service fee if you buy your groceries on-line, or if you pay your taxes on-line. On the contrary, the fact that on-line is more convenient and reduces paperwork should make it cheaper, not more expensive.
It's especially pernicious for events or services where you have to book on-line - where there's no other way of doing it. The market should react against these charges, and takes its business elsewhere.