With Google Custom Search, you can harness the power of Google to create a customized search experience for your own website.
So yes, Google does exactly that. You might have a point if it was the site owners themselves creating the search boxes, but Google offers large choice of tools to do exactly that.
On top of that Google also pays shareware and freeware authors to bundle Chrome in their installs, just like BonziBUDDY and all those other adware and spyware apps used to do.
On top of that it also directly inflates the usage amount as now there's 10x more hits than with other browsers.
It's also dubious that Google boasts their market share with these inflated numbers...
And what if one of the search results contain child porn or something else illegal? That's a nice way to get you to be suspect and your home raided.
It seems that Net Applications tracks more accurately too, because they ignore Google's inflating tricks:
IE at 54%, Firefox at 20.20%, and Chrome at 18.85%