Most basically: French, English, and German Jews were not permitted to own or hold land. Once cities start to get going, they were also not allowed to earn citizenship. That's a quick way to eliminate them from the legal power structure. (And explains somewhat the "moneylender or merchant" stereotype.)

As to rebellions: there is at least one case of the Jews of a town arming themselves to fight against what sadly turned into another massacre, so we know that (at least sometimes) they had armor, weapons, and the knowledge to use them. But Jews always remained a numerically small enough population that it was feasible for an urban center to expel the community altogether. As non-citizens and non-landholders, they lived in a place expressly at the will and whim of the political ruler, and signs of trouble--real or invented--got them kicked out very quickly.

I'd also like to suggest that under the constant pressure on all fronts to convert to Christianity, remaining Jewish was itself an act of defiance.