It's Microsoft's operating system, if they want to pre-install certain apps, why not?
There's nothing fundamentally wrong with Microsoft pre-installing apps, just like there is nothing wrong with Apple pre-installing apps on OSX, or Sun on Solaris.
That comparison does not work. Microsoft pre-installing their applications, or tweaking their OS such that their applications provide a better experience is anti-competitive because it lets Microsoft utilize their monopoly to prevent competition.
Google is not preventing any other search engines from gaining popularity. People go to google to find the most relevant answer to a particular thing, when the top result is consistently a spam knol, people won't go there to search anymore.
The concern with Microsoft wasn't that they used their OS monopoly to unfairly compete with other operating systems, it was that they used their OS monopoly to unfairly compete with other applications (eg. IE vs. Netscape).
The concern with Google isn't that they might be using their search near-monopoly to unfairly compete with other search engines, it is that they might be using their search near-monopoly to unfairly compete with other websites (eg. Knol vs. Wikipedia).
Google's heading in the same direction as MS. They'll probably end up in the same court room in Washington DC few years from now.