I don't think that is either funny or worrisome, at least to those somewhat familiar with credit card processing.
The way credit card processing fees work is that there are two kinds:
1. Per transaction fees, and
2. Percentage fees.
Not all per transaction fees apply to every transaction but if one does it is the same amount on every transaction. Not all percentage fees apply to every transaction, but when they do the amount is a percent of the charge amount, with the percentage the same for every transaction.
The big transaction fee is the "authorization fee". For a small merchant this might be $0.25-$0.30. If you are bigger they might give you a lower fee. I work at a company that is small now, but had a brief period of high sales and we were given $0.20 which thankfully has stuck. I've read that this can go as low as maybe $0.15 and perhaps even lower for really big merchants.
Another transaction fee is the AVS fee, which is $0.02. You are hit with this on any transaction where you supply address information and ask the card processing system if that matches the on-file information for the card. MasterCard has a $0.0195 fee called the NABU fee, which stands for something like "National Brand Use", which we apparently pay for the privilege of using the name MasterCard.
For the percentage fees, there will be a certain base percentage you are always hit with, and then various others that apply to some transactions. For all but very large merchants the base might be around 2% or so. I'm not sure what it is for the very largest.
(The above is if you have a merchant account yourself and directly use a payment processor like Authorize.Net or Merchant e-Solutions (MES). If you go through someone one step removed they might simplify it into one fixed fee per transaction plus either a fixed percentage fee or a tiered percentage fee system where a given charge gets one of the tiers. Apple almost certainly does not go through an intermediary like that. They either go through someone like Authorize.Net or MES, or maybe even are big enough to have access at an even lower level).
Anyway, the thing about this is that when you process a refund all that is guaranteed is that the credit card user gets their money back. Those fees you paid to have the charge processed? Some of them stick, such as the authorization fee. Furthermore, the refund itself is a transaction that will incur some of the per transaction fees (I don't think it incurs any of the percentage fees but I'm not absolutely certain--credit card processing bills are often extremely confusing and I've never been able to figure out from looking at the bills from at least 5 different processors we've used exactly what fees apply).
Assuming that most Apple app sales are $0.99, and taking into account the processing the refund will incur at least some fees, and allowing that Apple certainly gets better rates than I've ever seen, I can still easily believe that the net fees Apple pays on a combined $0.99 charge and $0.99 refund are in the ballpark of $0.30.
And since the whole freaking credit card system is set up, or at least appears to be from a merchant's point of view, to make sure that of all the parties involved in a transactions--the customer, the merchant, the merchant bank, the payment processor, the credit card companies, and the issuing bank--it is the merchant that bears the costs when anything happens that is going to cost someone money, nearly everyone who accepts credit cards as payments reacted to the claim that Apple keeps the 30% with "...and in equally unexpected news, the Sun rose this morning".