Buses in Israel are not segregated. There are, however, a few hyper-religious groups there, including ultraorthodox Jews -- in that society men and women keep separate for many things, including religious services (the reference the passenger made to "not being in a synagogue" reflects she knew this). The bus company designates a small number of buses for their use where the separation of men and women is the norm -- it is not the whole system. This bus was not one where the pax were to be separated, but one of these hyperrligious fanatics got on and caused trouble. What happened to the woman is wrong, but it is reflective of a small sect of people, not the country or the transportation system. If the OP had read the article he links to, he could have noted this, rather than implying that Israel is a segregated state.

There are neighborhoods in Jerusalem (populated by the same Ultraorthodox sects) where you are not permitted to drive on the Sabbath -- they throw stones at your car if you drive through. It isn't sanctioned, but people there know not to bother the unltraorthodox in their neighborhoods. In most places you do what you want, just not on those small areas.