Does Microsoft charge you a fee to develop and sell an app? No. But once you're locked into the iApps, iBooks, iTunes U, iUniverse - Apple gets its 30% off the top. And no alternatives are allowed.
What did Visual Studio Enterprise cost last time I looked for a small company (like a start up)? $1600 a pop. More than what's needed for a Mac Mini, an iPod Touch, and a Apple Developer License/Cert.
The same tools (XCode) cost $5.
(And you'd still have to pay for your hardware/OS on top of that $1600). And that's not counting MSDN fees, either.
Make no mistake: Microsoft milks its marketshare of developers just as much as anyone else. It's just a different way of pricing.
If you want to sell your mobile app in Microsoft's Marketplace, then yes. They charge the same as Apple does in the iOS App Store.
If you want to sell your desktop app in Microsoft's Marketplace, then yes. They'll charge the same as Apple does in the Mac App Store.
If you want to sell a desktop app outside of Microsoft's Marketplace, then no, that's free. Just like it is on the Mac.