I think its fair to say that Microsoft Windows is a different product entirely. Microsoft's business model literally a monopoly (100% install base) and they were willing to make different trade offs to get there. Interestingly though, the OS cost money--not free. So to run that "free" software, you had to pay MS money for the privilege.
iOS dev tools may be cheap. But that's not point. Apple has invested billions into that ecosystem. And to foster adoption, Apple's licensing model allowed for "free" software. But that was funded by the revenue collected from non-free iOS apps.
1990s-era Windows was a sort-of monopoly -- MS had a monopoly on Windows, and Windows ran on the substantial majority of PCs, and PCs were much of the market. But users could also get a Mac or one of several Unix-ish machines or an OS/2 machine or a BeOS machine, etc. So MS's actual monopoly was on platform that developers needed to target to make software to run on Windows machines.
Right now, Apple has a monopoly on the software running on iPhones and iPads and a near-but-not-complete monopoly on software running on laptops and desktops and Mac Minis. And there are plenty of users of various Android phones and even a handful of devices that are neither iOS nor Android.
So what's the difference? Apple wants to take a cut of gross sales of software targeting iOS, even in cases where Apple is uninvolved in the distribution of that software, and even when that software actually targets a platform-agnostic system and that system knows how to target iOS. Microsoft did not.
iOS dev tools may be cheap. But that's not point. Apple has invested billions into that ecosystem. And to foster adoption, Apple's licensing model allowed for "free" software. But that was funded by the revenue collected from non-free iOS apps.