What Microsoft did was in fact so much worse than what Apple is doing that the DOJ sued them for it and won.
I think the reason for the vitriol on this particular issue is that Apple is doing something that computer geeks don't think is correct, and computer geeks can't handle it when people do things "wrong".
Your first statement can't be judged yet. If all Microsoft had ever done was the IE thing, they wouldn't have sued. They had a pattern of anti-competitive behavior and that was the most egregious and well documented example so the DOJ went with it. Apple over the last few years has been fairly anti-competitive, this won't push it over the edge but it is another straw on the camel's back. So lets look back in 10 years and see what happened.
And the 2nd statement could be applied to the whole Opera sueing MS over browsers in the EU recently, or even the IE/Netscape thing back in the day.
Honestly I think it is more people don't like being told they have to waste time and money giving up projects/products they started and learning the tools Apple is arbitrarily forcing them to use. That is money out of people's pocket and you will find that pisses people off a lot more than anything else.
Acting anticompetitively to support a monopoly is what is against the law.
If the DOJ is up on Apple in 10 years, it'll be because their policies from today are so successful that they come to absolutely dominate the market. In which case, it would have been practically actionable for them not to have served their shareholders by pursuing those policies.
I think the reason for the vitriol on this particular issue is that Apple is doing something that computer geeks don't think is correct, and computer geeks can't handle it when people do things "wrong".