For large financial institutions, they move money in different and less expensive ways. For example, ACH fees are a tiny fraction of the cost that you use when you move money by credit card, and they're almost frighteningly easy to initiate (there is 0 authorization for these). It's just rare for the banks to expose a way to do ACH for you except in the specific case of billpay (and even then, many institutions handle these as mailed checks rather than ACH).
The idea that finance has to be hard with big ceremony in order to be secure is a clever ruse by big banks. They're not content with the large amount of security-from-competion that regulation gives them. They want your trust, and they're not afraid to scare you into believing that they're the only option.
I really don't believe it's a ruse, or even that the fees are that large. They're large for small businesses - and that's far from the only place where small businesses have trouble competing with the economies of scale larger players can use.
Interchange fees in the US are some of the highest in the world, and rising. They are a lucrative revenue stream for banks (iirc, ~$40 billion annually). See this piece by Felix Salmon for more: http://blogs.reuters.com/felix-salmon/2010/01/05/the-interch...
Thanks to the passage of Frank-Dodd, they should be dropping soon.