My four grandparents lived in the Empire when they were children, and they went out in the late 1920s, when it was clear that Communism wasn't going anywhere.
From the conversations I had with them, I can tell you that Nicholas II was an anti-Semite. The most violent pogroms, like the Kishinev pogrom in 1903, happened during his reign. Being an autocrat means that he was ultimately responsible for this, even if he didn't have any prior knowledge of the events in question. In "Nicholas and Alexandra" Massie mentions the fact that Konstantin Pobedonostsev was his mentor, like he had been his father's, and he instilled anti-Semitism in both.
On top of this, the Empress herself had her anti-Semitic issues as well, and she was not exactly loved by her Jewish subjects.
The fact that European monarchs and the people in general were anti-Semites, as they had been for centuries, doesn't justify that the Emperor and the Empress followed that line of thought, because they had a greater responsibility (again, along with the rest of the crowned heads of Europe and the democratically elected presidents in America): they had to govern their land, for which end they had Divine Right, and second, they had much better education than anyone else or so it seemed. This link
http://media.wiley.com/product_data/excerpt/83/04712076/0471207683.pdf may shed some light on the subject.
The "Protocols of the Elders of Zion", a hoax perpetrated during Tsar Nicholas II's reign, is still widely read in the Arab countries, for instance, even though the Russian government recognized the work for what it was. In the link above, it is said that it was none other than Grand Duchess Ella that promoted this libel. It appeared in 1901 in the Empire and it seems that the Okhrana was behind it. It is ironic that the Grand Duchess is buried in what is now Israel.
My grandparents and their parents and grandparents suffered a lot in the Empire just because they were Jews. They were not well off, lived in little "shtetls" of townships, in wooden shacks with dirt floors, and some winters the cold air would blow through the walls of their houses. The government pressed all sorts of absurd restrictions in their lives, and as much as the Tsar might have been a kind man otherwise, personally I think that regarding the Jews, history doesn't share that point of view.