specialks -
I'm not sure if you remember, but when you were asking a couple of weeks ago about getting the tickets with your Disney Visa (and thus, getting a discount), I was saying that you can call the main ticket phone number (which is what I think you did, right?) and order them with your Visa that way. That was the same phone # used by AP holders and DVC members to pre-order tickets and get their discounts. But I also said that if you got the discount, there would be a shipping fee of some kind which would cancel out some of the discount.
Ordering over the phone means there will be a shipping fee involved. But there was no way to get the Disney Visa discount online, as I understood it - and also as you were told by a CM online. (Didn't you say that you had chatted with a Disney person on the DLR website and they told you that you could not get a Disney Visa discount? And then I subsequently called the ticket phone # and spoke to CM Amy, who said that if you called the number you, indeed, could pre-order tickets and get the Disney Visa discount.)
So, basically, you can order online with whatever form of payment you want to use and get e-tickets and no shipping charge. However, I don't think you can apply a Disney Visa discount to online orders (someone correct me if I'm wrong), which was confirmed by that CM you spoke to. But when you order over the phone - and in your case, get the Disney Visa discount - there will be a shipping charge.
I don't know if that all makes sense, but I think that's what the explanation would be for why you were charged shipping and what it means!