I'm by no means defending the percentage they take, but I would suggest that it's a percentage because it's simple:

Pick 3 imaginary games for sale priced at $1, $10 and $100. Any one of those games could be a million download a month success, and any one of them could be a complete dud.

What flat rate would you suggest to:

* Pay the developer for their work (ongoing per sale)

* Review each game and ensure it meets store guidelines (once per update)

* Host said game regardless of how popular it is (ongoing)

* Process transactions for the game (ongoing)

The alternative would be pricing based on revenue tiers (similar to what Unreal Engine does now), which aren't known in advance and don't take global variance into account (USD$200 in Eastern Europe might be a month's salary).

Percentage is just simpler. It also means that they'd be taking a loss on every free app or in the case of Free-to-Download In-App purchase apps - until users start transacting.

Personally I would rather transparent pricing. For each service the store offers, add a cost of appropriate type and value for that.