I see (and respect) what you're saying, but something tells me this will be a little different. Honestly, I probably don't have any idea what I'm talking about, but it sounds as though Apple is going to have to do some quality control on these applications (to make sure they're void of any destructive coding) before they allow developers' apps to be hosted (on what I'm assuming will be iTunes). This could possibly allow Apple to charge for each individual application, regardless on whether or not the developer originally wanted the app to be free.
Mind you, of course I hope I'm wrong, because obviously I'd rather the apps be free