Before, the process for shipping an app looked like:
1. Obtain Xcode, either as a free download, or from your OS install media. (Apple just shipped Xcode along with the OS for a while.)
2. Develop your app.
3. Distribute your app directly to customers.
With iOS, the process for shipping an app looks like:
1. Obtain Xcode as a free download.
2. Start developing app.
3. Realize you need to test on real hardware at some point. Before Xcode 7, testing on real hardware, even your own, cost $99/year. With Xcode 7 you can do it for free, as long as you get an account and have Xcode fetch the certificates for you.
4. Submit your app to Apple for distribution on the store. If you did step 3 without paying, then you need to pay your $99/year here.
5. Wait a week or so for Apple to review your app. With luck, they'll approve it. If they find something they don't like, they'll reject it and you get to go back and repeat this process until you appease them.
With the Mac today, you have a few choices. You can go through the App Store, where the process looks much like the iOS process, except you don't have to jump through any hoops to test on your own hardware. You can go through Developer ID, where the process looks like the old Mac way, except you pay $99/year to have a signing certificate. Or you can keep doing things the old way, at no cost, but most of your users will get scary, scary warnings when they try to run your software.
The thing is that it's not about the tools being paid, but the distribution being paid and restricted. I can completely understand paying for developer tools. Until they went crazy, I was happy to pay JetBrains for some of their tools, for example. Your Windows tools required payment to use them for real work, and that's fine. But if you didn't want to, you could have used mingw or something like that, and done everything for free and without restrictions. This option is simply not available on iOS, and is being slowly ratcheted down on the Mac.