Jews by the time of the Holocaust had been heavily persecuted against, and in pogroms (anti-Jewish riots) for centuries. So as the Holocaust happened in relative slow motion, each gradual restriction on their lives: being segregated from public life and schools, wear the Star of David, relocate to the Ghetto, Jews often viewed them as simply another form of discrimination, which they were used to.
There is also a principle in Judiasm of enduring discrimination, of turning the other cheek. Add to this the natural human response, the will to survive that often overpowered their perception of the reality of the Holocaust. They didn't believe it was happening and they didn't want to believe.
There are notable exceptions. The Warsaw Ghetto Uprising in 1943, as well as the revolt at the Treblinka death camp and Jewish partisans that fought in both the Soviet Union and Poland. These acts of resistance were relatively rare, but they did take place.