It's impossible to conclude from the evidence presented that the antitrust action had no effect on the breaking down of Microsoft's monopoly. It's entirely plausible that the enforcement left them unable to respond as quickly to new markets as their competitors, leading to them beginning to get undermined a few years later. Abusing their monopoly in the PC OS market to get advantages in unrelated markets was in many complaints against Microsoft at the time.

It's entirely within reason to believe that had the Justice Department not been breathing down their necks that Microsoft would have used its monopolies to illegally squash the original iPod. There are plenty of examples of products that were well-made, innovative, and desired but didn't make a major market impact for poorly-understood reasons (WebOS comes to mind). It's not at all obvious that the iPod was bound to succeed; if all those amorphous outside factors hadn't gone its way, we could be sitting around discussing how the iPod was a repeat of the Newton, and how inevitable it was that Microsoft finally cracked the the MP3 market with Plays4Sure.