I expect it does include fees paid to Apple so that Apple would send search traffic to Google, and fees paid to browser vendors.
Our experience as a search results provider was that there was demand for a more 'functional' search capability (not casual searching) many of the techniques we used have been adopted by Microsoft in their Bing engine which has improved both their recall and quality with respect to Google results on highly contested searches.
I certainly agree that Yahoo! has made a number of missteps with their search technology. I talked with them once (post Marissa's arrival) and in many ways they were confused as ever about how search engines generate value for the parent company, but such things are rarely permanent.