It bugs the hell out of me.
I mentioned it elsewhere but I was recently relieved of £60 from BA, as I wanted to use an AMEX 2-4-1 and then book 2 x children MFU to J, neither of which could be done online.
I emailed BA and politely asked them to refund the money, but they told me they wouldn't. The other sneaky fact is that the agent on the phone never mentioned the charges, and incorporated them into the price quoted. Until I said the online price was slightly cheaper, to which she replied "oh yes there is an offline service fee built into the ticket price".
Why do the public have to pay a penalty for the shortfall of their website? The company I work for offers a web based booking tool for our products and we wouldn't even consider charging customers to call because of the shortcomings in our offerings