I'm a CPA who works specifically with software revenue recognition. It is one of the hokiest areas of accounting, and Apple's given reason doesn't surprise me one bit.
The Financial Accounting Standards Board (FASB) issued EITF 08-1 (some people call this The Apple Rule) a little while back, and that injected some reason into the whole thing. But it didn't cover every scenario.
If Ernst & Young, Apple's auditors, decides that FaceTime adds "significant functionality" to existing software, they can basically force Apple to go back and restate all the earnings related to the devices which will be upgraded with the software. This is because Apple didn't foresee offering FaceTime when they originally sold the software to consumers.
If Apple charges SOMETHING for it, then this issue becomes moot.
Why E&Y views FaceTime as significant, but not other updates, is unknown to me. But that is clearly what is going on here.
This gets a little more complicated since many of the devices were sold when Apple had a different auditor, KPMG, with sometimes very different opinions on this subject.
I don't think Apple would have satisfied E&Y by charging $0.01 for the update, since they don't typically charge that for other apps. It looks like Apple went with the lowest price they could charge that was typical, which is $0.99.
If you want some great reading on the subject (or if you want to push yourself closer to the edge of sanity), Google SOP 97-2 and enjoy.
Thank you! All the whining about Apple just wanting more money was getting annoying.
Also, the App Store being free doesn't require a restatement of earnings because of their 30% commission covers the earnings requirement