The issue here is that Google got to keep their jets at AMES at all, not that they got fuel subsidies. NASA sold them fuel the only way NASA knew how, and probably in full compliance with regulations. The issue is not with the fuel sales, but with Google being able to keep their jets their at all.
Anyone familiar with the area knows that AMES is much more convenient for a private plane of the size the Google Execs own than pretty much any other option. SFO, OAK, and SJC are all busy, and have various red-tape on them. Airports like SQL are too small for the google jets. Normally no non-NASA flights can be at AMES. There are no Apple Jets, no Cisco Jets, no Facebook Jets at this airport. Google attempted to get around this by offering free instrumentation on their jets to NASA.
This is the first step in calling bullshit. This should have never happened. A few instruments does not make it a NASA project. Google should have never been there in the first place. Someone gave them preferential treatment using the instruments as an excuse.