That's the whole point - making it not too affordable so that users browsing the App Store don't have to wade through too many nonserious hobbyist apps. Lowering the bar too much hurts users.
I mean, all this is about mass distribution to unsophisticated consumers, not hobbyists - without that $99 you can work on your hobby projects and you can share them with other hobbyists; the only place where that $99 is a barrier is the distribution channel to non-hobbyist users.
In essence, the message from Apple to hobbyist developers is to 'go big or go home' - if you're seriously developing something useful, then $99 is insignificant; and if the time effort you're putting in that app is not much, much more than $99 then it's reasonable to draw a line that they don't want such hobby projects on the app store. You can experiment with it and share it in small communities and when (if!) you think this project has become serious enough to go beyond hobbyists to the mass market, only then you need to pull out that symbolic $99 to demonstrate that you mean it.
