Emperors Theodosius II and Honorius reaffirm all the previous laws against Jews, heretics and pagans. Jews will be protected from people acting in the name of Christianity, but Jews aren't allowed to convert Christians.
According to the law:
"Known and published are decrees which suppress the spirit and audacity of the abominable pagans, Jews, and heretics. We gladly repeat the law.
In response to the pitiable supplications of Jews, we will punish those who injure or persecute them under the pretext of venerable Christianity. From now on, no one shall seize or burn their synagogues.
Nevertheless, the Jews themselves will be punished by confiscation and exile for life if it is discovered that they have circumcised a man of Our faith." [CTh 16.8.26]
It's unlikely that the emperors would feel it necessary to protect Jews from violent attacks being committed in the name of Christianity if this weren't an ongoing problem. Christian churches don't need imperial protection from pagans acting in the name of their religion — it's only Christians who are committing crimes in the name of Christianity.
Given the extent to which they are being favored by the state, they may feel that their violence will be protected as well.