Judaism's history has of course been replete with anti-Semitism, including Crusades, pogroms and the ultimate anti-Semitic incident: the Holocaust. In today's world, anti-Semitism is often more subtle. It hides behind terms like anti-Zionism and human rights (when discussing Israeli Palestinian relations or anti-circumcision laws). Occasionally, there are outbursts of anti-Jewish violence, but these are generally dealt with by government authorities (the Arab world notwithstanding).
Is it possible that the administration of Yale thinks these expressions of anti-Semitism are not worth researching?
Some have suggested that the reason that Yale closed down the institute is Arab protests against a conference held there last year which discussed the dangers of anti-Semitism in the Arab world. Yale's official reason was that YIISA had failed to "serve the research and teaching interests of some significant Yale faculty and . . . [to] be sustained by the creative energy of a critical mass of Yale faculty." One of the reasons to doubt that this is the real reason is that Yale publicly courts Arab donors. The Washington representative of the PLO publicly condemned the institute and asked for disassociation from the university because of its existence.
Chances are that Judaism's history will not be majorly affected by the closing down of the institute. Clearly the university does not believe that anti-Semitism has disappeared from the world. Either it was seriously concerned with the quality of work being done there or it bowed to pressure from potential donors. In either case, the decision hardly seems worthy of all the attention it has been getting.