Monetarily they were just slapped on the wrist, but operationally they were not. Talk to people who worked or work at Microsoft. They've been restricted from many (arguably good) moves with their software because of the Justice Department's lawsuit.
Many are hopeful that Microsoft can start to really innovate again now that the consent decree has recently expired.
I have indeed heard the whiny, victimized rants of some low-level employees ("Woe is us!"), however by and large I think it's nonsense. The restrictions and oversight the DoJ put on Microsoft were well known and are public record. They aren't secretly restricting them beyond what we all know.
Microsoft did get but a slap on the wrist, and rightly so. Though it's worth noting that had Microsoft received the punishment so many sought -- the breaking up of the company -- the parts would almost certainly be worth much more than the whole right now.
Microsoft's problems are Microsoft-created. Like RIM, Microsoft was more focused on entrenching the status quo than planning for the future.