The New York Times has a story about Microsoft fighting off Google's antitrust complaints against Windows Search built in to Vista.
"Google complained to federal and state prosecutors that consumers who try to use its search tool for computer hard drives on Vista were frustrated because Vista has a competing desktop search program that cannot be turned off. When the Google and Vista search programs are run simultaneously on a computer, their indexing programs slow the operating system considerably, Google contended. As a result, Google said that Vista violated Microsoft’s 2002 antitrust settlement, which prohibits Microsoft from designing operating systems that limit the choices of consumers."
I'm not sure if this can be compared to the antitrust case against Microsoft in the late 90s (See how Microsoft botched the antitrust case in the late 90s). Back then you had a case of Microsoft threatening Compaq computers with a termination of their Windows license agreement if they dared feature the Netscape browser and not Microsoft Internet Explorer. In this particular case, the mere existence of a competing search engine from Microsoft doesn't necessarily prove antitrust violations unless someone's arm was being twisted to not feature Google Desktop or risk losing their right to bundle Windows. I would venture to guess that it's currently unlikely that Microsoft would be so bold and reckless as it was in the late 90s with all the legal troubles that remain to be settled.
Furthermore, it is quite trivial to shut down the Windows Search Service. In fact we don't even need the user to manually do this, there's no reason the Google desktop installer can programmatically shut down and disable the Windows Search service (with the user's permission UAC elevation) if it wants exclusive ownership of search on the desktop. But the newest Windows Search Service seems to be performing fairly well and I've been using it for the last 5 months without problems and this is coming from someone who exclusively uses Google for web searches. Google has also had some security problems with the desktop search product not to mention some controversial features that took internal company data and sent it out to Internet Servers. Google's response was to offer an enterprise product for purchase that would globally manage those features which angered some enterprise IT departments.
One other major factor is that Microsoft - unlike the late 90s - is actively lobbying the Government. According to the same New York Times story:
For its part, Microsoft, which spent more than $55 million on lobbying activities in Washington from 2000 to 2006 and substantially more on lawyers, has become a more effective lobbying organization.
This is a hard lesson learned from the late 90s when Bill Gates personally hated politics and avoided Government while Microsoft's opponents lobbied hard in Washington. Microsoft stayed home while the Justice Department under Bill Clinton started its antitrust investigation of Microsoft and that oversight (along with its arrogance and refusal to settle) nearly caused Microsoft to be split in two. I'll have to leave it up to you to decide if this latest antitrust complaint from Google has merit or if Microsoft has better lobbyists. All I know is that Google is no stranger to Washington politics.