The iOS app, which we're talking about re: the Apple developer fee, is most certainly a commercial endeavor. The FOSS desktop app doesn't change that.

Right, but I assume it went something like this:

1. Users nag developers about not having an iOS app

2. Developers start considering creating the iOS app. Finds out they have to pay $100 a year, on top of spending time to develop the app.

3. Developer decides to charge the users that wanted this app at a price where they can be fairly sure to at least regain monetary expenses.

This seems fair to me.

The author didn't just make it out of the good will of his heart, he wanted to turn a profit and set out to make money off the iPhone version from the outset. The $100 fee is a triviality in the face of the hundreds and hundreds (thousand, even) of hours it takes to create and maintain Anki on iOS. You don't have to look far to see the development of the native version of the iOS app was even contracted out, for pay. It was taken very seriously.

Not all FOSS software developers are against making money. Often FOSS projects can be a starting point to launching a commercial product or service, whether it was originally intended to be one or if a long-time hobby project happened to grow to the point that making a business around it becomes a viable new option.