Someone ends up paying Apple either way. On the App Store, that person usually ends up being the developer. With the new framework (stupid as it may be), developers can choose to externalize that cost to users and make an example of how ridiculous it is. With high-demand apps like emulators, it's easy to attract users and directly expose them to the limits Apple imposes on them. That's a great vehicle for change, and I fully expect Apple to backpedal on the Core Technology Fee once it attracts broader scrutiny.
It makes perfect sense to me that paying $99/year for the App Store is cheaper than $0.50/install. But you shouldn't have to pay anything to install Free Software in the first place, so I can also see why some people would consider protesting Apple's policy to be invaluable.