The problem with Google, as far as the US Government is concerned, is that it is not a government regulated monopoly. They fear anything with such vast scope and influence / power, that they don't have a certain level of direct control over.
The purpose of pursuing Google on anti-trust is to bring them under supervision of the US Government. The same reason the Feds were interested in Microsoft. It surprisingly takes very little to cause anti-trust problems for a major company, as little as one powerful senator dedicated to the issue. Google will be brought under a consent decree in the next few years most likely, and by the time the Feds get around to doing that, the market will have likely already made Google's dominance in search a lot less important.