It's interesting to contrast this to today's Apple. (Consider that Java programs also ran terribly on Windows; there's a legitimate user experience argument that Java "should not have been allowed" until they could make it take under 10 seconds to start up.) While Apple is certainly not a monopoly, I think the moral objection -- at least the one I had -- to Microsoft's behavior was not so much from abusing their monopoly but rather that zero-sum behavior is wasteful in our non-zero-sum world. That is, seeing someone spend their energy to destroy others rather than trying to out-improve their competitors is always a downer, even if they're nobody.
But while people complain about Apple, it's only a few people; users don't care at all (aside from the blue lego), and even most developers affected by Apple shenanigans retain the necessary cognitive dissonance to rationalize it. Why? What I think the important difference between Microsoft then and Apple now is that Microsoft's products just weren't very good.
That is, once we're at a state where we're ready to blame, we talk about it in terms of the morality and what is good for the world; but we only get to the point of blaming when we're unhappy as consumers. (Consider how quickly people forgive Facebook for the variety of privacy fuckups they've made -- it's because, even with the bad, people love using Facebook.) It's the same reason nobody's too upset that it's Adobe in particular getting cut out: as a user of the web, I know that Flash just isn't very good.
Rather than arguing now, Adobe could have helped their case more in the past by working with browser vendors to improve their plugin -- making their plugin not be the top source of crashes for browsers (I found it hilarious that, before they had finished the work to move plugins out of process, Safari had extra code specifically to blame Flash when it crashed), not dropping the ball on protecting their users, leading the pack on GPU integration to make Flash outperform the
<video>tag that browser vendors effectively introduced as a workaround for Flash's poor integration.
This probably wouldn't have directly helped the current situation with Apple (whose primary interest, public statements to the contrary, is more in locking in developers and users to their platform). But if both users and developers loved Flash, it would mean that Flash would have been more of a fundamental piece of the internet rather than that thing we grudgingly tolerate to make YouTube work, putting Adobe in a stronger bargaining position with respect to new gadgets.
(More fundamentally, I have long wondered about the wisdom of a company who has nearly tied their success to an operating system distributed by a company that historically repeatedly shown that they only grudgingly allow third-party software for niches where they haven't yet had the time to write their own version, e.g., but maybe that problem is endemic to all operating systems.)