Although AH frowns on one-word answers, this fact is much of the OP's question can be answered with a single word: antisemitism. Judeophobic ideas and discrimination was common within imperial society and was incredibly pervasive within the state bureaucracy. This primed the state to associate Jews with all sorts of subversive activities such as the political underground.

Despite Alexander Wielpolski's initiatives during the Great Reform period to emancipate the Jews of the Western Provinces, the empire maintained a highly restrictive regimen of control and discrimination against its Jewish subjects. The official categorization for Jews was inorodtsy, which roughly translates to "resident alien subject" with overtones of otherness and a lack of civilization. Jews, even if they lived in the shtetl for generations, were thus still treated as transient outsiders who existed at the sufferance of the tsar. Most of the empire's Jews lived in what was known as the Pale of Settlement- see this map- and could not legally leave the Pale. Those Jews who could leave the Pale usually were either professionals or those who had somehow proved loyalty to the state such as through conscription. The barriers though for professional advancement for Jews were often quite high, even for converts. Most Jews were locked out of access to higher institutions of learning and the imperial bureaucracy.

Not surprisingly, this panoply of discrimination did foster a hostile attitude among some Jews towards the Romanovs. There were a number of Jewish intellectuals like Shloyme Zanvl Rappoport were active in the various underground political associations such as the narodniks. The Western Provinces were also the epicenter for much of Russia's industrialization and Jews were part of the regions' growing labor activism. The Jewish Bund was one of the larger socialist parties within the Western Provinces and it recruited among the heavily-Jewish cities like Lodz or Odessa. On the other end of the socio-economic divide, there were a small number of Jewish entrepreneurs who capitalized on industrialization such as Brodsky "sugar barons" who pioneered methods of producing cheap beet sugar for Russia's growing consumer base. Ironically, antisemitic discrimination against Jewish professionals fostered the phenomena of the Jewish industrialist. Educated or successful Jews found few outlets for their children, so industrialization and other business investments were one of the few career paths open to them. But such prosperity was always precarious and even great wealth carried little political capital. The Brodskys had to fly in the teeth of considerable state opposition to construct Kiev's Great Synagogue. Zionism also received a great deal of currency in light of pogroms and the rejection of Jews by most gentile nationalists such as the Poles.

But Jewish opposition to tsardom was not absolute nor did it enfold a majority of the Empire's Jews. Jewish intellectuals in the underground were always outnumbered by their gentile colleagues. This was in keeping with the larger trajectory of radicalism in this period in that Jews were never a majority of radicalism's intellectual vanguard. Moreover, a number of Jewish radicals did not really consider themselves Jewish in either a religious or an ethnic sense. Trotsky never really self-identified as Jewish and his writings often critiqued the parochialism of Jewish institutions. The Bund was an explicitly Jewish socialist organization, but it also had a very freighted relationship with Judaism as a religious practice. Most of the empire's Jews were not Bundists or followed Trotsky's path. There were long-standing traditions of shtetl political leaderships not wanting to rock the political boat. The mainstream of most of the Empire's Jews was apolitical. Much like the fictional Tevye the Dairyman, most Jews were much more concerned with scrounging by under severe political and economic restrictions than wanting to tear the tsarist system down.

But while most of the empire's Jews were apolitical, this was not the opinion of the Russian state hierarchy. Jews were a natural underground enemy for the empire's secret police and other security organs. Most of this suspicion of Jews was independent of Jews' own involvement with these various underground groups even though studies of the ethnic origins of political prisoners showed Jews to be a distinct minority. A good many within the secret police considered the Polish revolt to be the result of a Jewish-Pole alliance to overthrow the empire in the Western Provinces. This conspiracy theory though failed to account for the fact that the Polish nationalist movement was arguably as antisemitic as the Romanov state. The presence of Jews among Western Marxists further added the idea that Jews were natural underground leaders. So when the state was predisposed to find Jews as disloyal they inevitably looked for confirmation of this bias.

Some of this confirmation was fabricated out of thin air. The most famous and pernicious evidence of this was the pamphlet The Protocols of the Elders of Zion which plagiarized the book Dialogue in Hell Between Machiavelli and Montesquieu by Maurice Joly and other existing works while adding in a number of antisemitic invective. Although there is no clear evidence about the secret police's motives in concocting this forgery, the general historical consensus on the Protocols is that they were part of a larger plan by the secret police to discredit various underground radicals and to further steel the Russian peasantry's loyalty to the tsar. The widespread antisemitism within the empire and beyond made the pamphlet a sensation. In Poland, this Protocols buttressed antimarxism in the bitter political fights of the twentieth century and helped coin the term żydokomuna (Jewish communism). Nicholas II actually read the Protocols after his abdication and thought they were a marvelous explanation for the tragedies that had befallen the dynasty and Russia over the war.

That Nicholas II believed a forgery widely circulated by his own secret police during his own reign is not only a testament to the bureaucratic chaos of the late imperial state but also the pervasiveness of antisemitism among the Russian elite. Jews became a convenient explanation for any misfortune the empire suffered and that included 1917 and Lenin.

Sources

Klier, John D. "Why Were Russian Jews not Kaisertreu?." Ab Imperio 2003, no. 4 (2003): 41-58.

Weeks, Theodore R. From assimilation to antisemitism: the" Jewish question" in Poland, 1850-1914. DeKalb: Northern Illinois University Press, 2006.

Zimmerman, Joshua D. Poles, Jews, and the Politics of Nationality: The Bund and the Polish Socialist Party in Late Tsarist Russia, 1892–1914. Univ of Wisconsin Press, 2004.