I suspect Apple is trying to build up the Mac App Store. I doubt they care about the money they get from Xcode or Facetime ($0.99).
Perhaps it sets up an expectation for the consumer - a small utility should cost about $0.99 and that a larger application should be about $4.99.
This gets consumers in the habit of paying for software they might expect to be free, motivating developers to use the Mac App store and builds up an ecosystem to match the iOS app store.