Yes, Microsoft had 90% of the desktop OS marketplace, and did use that dominance to gain an edge in other markets. But despite that large market share, their leverage was kind of limited by the platform being open. Apple, on the other hand, has unlimited technical leverage. They can make up whatever anti-competitive rule they want to, and enforce it totally.

When Microsoft chose to neglect the web after IE6, it didn't take that long for competition to work around it. When Apple chose to neglect Safari in exactly the same way (and probably for the same reasons as Microsoft did with IE6), that was it. There was no workaround, nor any way for anyone to compete with a better browser.

PC games are a >$50 billion market, with Microsoft only getting a small slice of that. That's because Microsoft wasn't just able to outlaw direct installs nor competing digital games stores. Games for Windows Live had to compete against e.g. Steam, with the predictable outcome. The size of the iOS gaming market is comparable. Apple collects a 30% cut of it, and will do so indefinitely. Competing with them is literally impossible; nobody else can make a different app store offering better terms or a better user experience.

Apple is at around 60% market share in the US. The difference between 60% and 90% is a minor difference in scale. The difference between Apple's absolute control of iOS vs. the limited control that Microsoft had over Windows is a difference in kind. Apple got to choose whether competing software was even allowed on the platform. They could opening up special capabilities to only their own software, and actually enforce that (unlike Microsoft, whose undocumented APIs could still be reverse engineered). They can charge their competitors a 30% cut of revenue, while obviously ignoring it in their internal accounting for their own competing businesses.