The story behind the Protocols is quite long and tangled, and much of the evidence debunking it is either in things we'll never see now like old newspapers that no longer exist or in a foreign language or both. Wiki has a pretty good summary with over 70 footnotes and cross references, but if you don't trust Wiki, there are several books currently available which are perhaps a little more readable: The Plot: The Secret Story of The Protocols of the Elders of Zion; The Lie That Will Not Die: The Protocols of the Elders of Zion; and several others. There has always been anti-Jewish sentiment, as in that old Greek myth. The Protocols got its start in the 19th Century from various screeds against the Jews, but much of the text itself is actually plagiarized from a play and another book.

Definitely Judaism changed when the Temple was gone, because Judaism had always been rather unique in being centered around one building where God actually dwelt. That goes back to Moses and the Tabernacle, though. This was why only the High Priest could go into the Holy of Holies and that only one day a year, the Day of Atonement. And animal sacrifices could only take place at the Temple under strictly regulated procedure. No Temple, no sacrifices. The Pharisees, Sadducees, and Zealots, in their rebellion against the Romans, brought their own house down. That's an epic story of why politics and religion can't coexist. Since the First Century, it's all been the remainder of the scattered rabbis trying to hold their traditions together. The Talmud developed by the 5th Century as it is now, that's another long and tangled story.

The situation in Russia and the pogroms also had to do with politics. The Jews were a handy scapegoat for failures of the Tsars. And it should be no surprise that they had their own political alliances. Some of the worst enemies of the Jews have been other Jews.