There are a lot of factors at play. The first is that in the newly Christian empire onward, the Jews were a convenient scapegoat for all kinds of weirdness. I can't speak to the pre-conversion historical problems, but late antiquity onward they become a common sort of "other" to blame things upon.

Not only were they seen as the catalyst for the crucifixion of Jesus Christ, they also tended to be in close-knit communities that discouraged outside influence and involvement, further "othering" them as a group. This was compounded by the early Church prohibiting Christians from charging interest on loans to fellow Christians, leading to the rise of the popular imagery of Jewish moneylenders causing a lot of problems. Over much of the medieval period, kings and rulers made a tidy business of banning all Jews from their lands, thus forcing a forgiveness on these loans, which were often to the nobles and crown anyway. Eventually they'd let the Jews back in for a fee, collecting more money.

Once the Black Death surfaced, the outsiders in the community sometimes were seen as the cause. While no one could be certain what was killing people off at such a horrifying rate, people wanted someone to blame and the reclusive Jewish communities became a natural target. Blood Libel against them had always existed, and the pogroms of violence against Jewish people increased a lot during this time. Through the modern era, you see a lot of variations on this same theme.

The short answer is that they were a group that was easy to blame things on because little was known about them by outsiders to the group and they were often doing unpopular jobs. While it wasn't exclusively Jewish groups that saw this kind of blame and violence, they were consistent enough as a unified group to be seen as a problem for those who wanted an easy answer for what is going wrong. It's a shame, but humanity seems to like to see outsiders as in the wrong rather than trying to understand them instead.

Hiya, not discouraging any new answers coming in, but you might find this post by /u/yodatsracist interesting and helpful.