Israelis and other people calling for an academic boycott against Israel do not necessarily blame Israeli universities in general or any particular university for inappropriate acts. They are calling for an action against the State of Israel. And note that an academic boycott was one of the actions the UN took against South Africa, so extending this idea to cover Israel too is really natural. My own preference is for a targeted boycott, against Israeli institutions which support what is happening in the West Bank. An example would be Bar Ilan university and the Ariel College (if it has any contact abroad).
from the article: Boycotting the boycotters