I agree with Tsarfan, but would add in the classic "Jews are Christkillers" accusation. If this concept continues to be believed among many of today's "good churchgoing people" (who also, by the way, assign Jews much of the responsiblity of the Russian Revolution and other ills) why is it so difficult to come to grips with a man who lived one hundred years ago thinking along the same lines?
The last tsar was, in many ways, a cosmopolitan fellow, but deep down he continued to retain the prejudices he had been taught by his tutor, probably by his father, and certainly by the general culture surrounding him during his formative years. In addition, he had the luxury of being distanced from the evil that was inflicted on Jews. If he had witnessed the horrors of a pogrom, would Nicholas have changed his attitude? I don't know. I would hope so.
I have always liked, and continue to like, Nicholas II. But just as I can understand (though not condone) WHY he had anti-Semitic leanings, I also cannot twist things around in my mind so as to declare him innocent of anti-Semitism.
It is through learning about anti-Semitism as practiced not only by goons such as Hilter, but also by far more appealing individuals such as Nicholas II, that we learn how prejudices take hold and are accepted by "good" people who are complacent or even swear fealty to monsterous governments promoting murderous policies.