Why is Israel the Obama Administration's Litmus Test?

The NYT reports that Charles Freeman Jr. was not appointed to a top intelligence post specifically because of his critical stance on Israel:

"Mr. Freeman had long been critical of Israel, with a bluntness that American officials rarely voice in public about a staunch American ally. In 2006, he warned that, “left to its own devices, the Israeli establishment will make decisions that harm Israelis, threaten all associated with them and enrage those who are not.”

I find the trend of Israel determining major decisions fascinating and disheartening - first the 2nd Conference on Racism, now this. Would Freeman's views on Israel really affect his ability to do his job? What does this mean in terms of the larger atmosphere of the administration and the country? It seems to me that the U.S. government feels that it can not criticize Israel at all, when I believe that criticism and guidance is exactly what Israel needs... Thoughts?