That's because you're paying the lisencing for the product. Microsoft is a software company, they make very little hardware (And most of their hardware is just comprised of peripherals and concept products). They have to make money somehow, so they do this by selling the lisencing to their OS. Mac is exactly the same, $30 and upgrade. Windows just charges more though because their OS upgrades take longer to come around and usually take a bigger step forware (I'm not dissing Mac by saying it's slow to evolve or anything, I'm just saying Mac takes slow and steady steps, while Windows takes a large leep, but only every few years).
iOS used to cost money to upgrade on iPod Touches, but this generated very little revenue, and mostly irritated iPod Touch users, so Apple stopped. As only Apple makes devices that use Apple OS's, there's no licesing fee.
Andriod is 100% open scource and free, meaning anyone, including you, can just go and download it free. They don't charge licesing fees, instead, making money off increased ad traffic.
Windows Phone does charge a liscensing fee, meaning every WinPhone device sold, the manufactor has to pay a small fee to Microsoft. Of course, to stay competitive, they don't charge upgrade fees.
Going back to conventional x86 desktops, when you buy one at a store, the license for that computer has already been paid for by the maker, so if you build your own, you have to pay Microsoft for a license. If you wish to upgrade, you must pay for the right to use that new OS, through the means of paying for a new license or upgrade fee.
I imagine Windows RT/WoA wil follow this same principle, because it's a more full fledged OS (But it can't run legacy programs). Of course, I would imagine the upgrade fee would be much smaller, but we can't know, becuase this will be the first time Windows has ever supported an ARM device.