Of course IF MS Flight *will* have an integrated Marketplace curated by Microsoft, it will require agreements between Microsoft and 3rd parties.
They do it already for Indie games made by individuals on the Xbox Live Marketplace, I'd take it for granted they'll do it for an hypothetical similar marketplace inside MS Flight. Again, assuming there will be one in the first place.
In any case, it's just the way the development world is going:
- Apple, which is now the most successful company in the IT world, is running a closed App store for the iPhone and taking a cut out of everything produced there, they started on the iPhone, but it has now being extended to the Mac too, and no sane Mac developer would ever *think* of NOT selling his own stuff there.
- Microsoft has already hinted that native Windows8/Metro apps will require developer certification and will be purchased on a curated app store.
- The most successful digital distribution platform for PC games (some might say PC gaming has been *saved* by them), which is Steam of course, also selects which developers to bring on, and obviously take a cut of every sale made there, and they represent about 70% of the digital delivery market on the PC
So yes, there's nothing unusual or strange about this, it's just the way the development world is going.