Microsoft only had about a 70% market share, there were other OS's that could be used. The only way people were prevented from entering the market was through patents. Otherwise, Microsoft could do nothing to stop anyone.
No monopoly prevents market entrance entirely, that isn't a requirement for it to be considered a monopoly.
It doesn't appear to be patents that prevented market entry, it was:
1. Trade secrets (as Mega points out). The develop source code, but what they deliver to customers is a black box that "just works".
2. Copyright - if you managed to steal their source code, you can't just copy/paste it and not get in trouble.
3. Integration - In many software systems, once they get large and expansive enough, it looks something like this.
Software bundle does process a,b,c,d, they are all tied together.
A competitor has to bite of a small enough chunk to make it feasible, so they try to create processb, for example, better than the monopoly. They do, they do it 2x better, for 1/2 the cost!! A clear winner. Yet it's 100% useless, and unable to compete. Because it can't know how to talk to processA and C efficiently, no customer would be able to use it. This goes on an on, to costs of changing systems, training costs, expertise, etc. It effectively prevents competitive market entry this way.
Not saying what's bad or good, just trying to point out what I think the software monopoly looks like. That MS email describing integration was spot on (obviously, they ruled an industry that way). Many software markets have similar dominance. Open access is starting to bleed over into old guard software of all types..but it's slow going.
It is not insane in large markets to consider forcing vendors to allow interfacing with their tool if it's part of a "flow". They don't need to give up the inner workings, just have it terminate in such a way that people can plug other software into it. As long as its evenly enforced, it's not terribly restrictive and it helps the market compete.