John 16:2

They shall put you out of the synagogue. The assembly of the Jews was called a synagogue, as was also the place of the assembly. For God had ordained that there should be only one Temple in Judea, where sacrifices were to be offered. And this could not contain all the Jews, nor could they all attend it weekly. Accordingly the Jews had one or more Synagogues in every city (in Jerusalem at the time of its destruction there were 480) which the people frequented weekly, only to pray, and to hear the Law expounded by the scribes. They seem to have been set up in the time of the judges. To be put out of the synagogue was accordingly the same as being excommunicated (see ch. ix.) But Christ here promised His Church to the Apostles, when the Jews excommunicated them.

But the time cometh, that whoso killeth you will think that he doeth God service. Maldonatus takes "but" to mean "because" from the Hebrew word ki being so translated by the LXX. Service, the service that is, which is due to God alone. Both Jews and Gentiles will offer you up as a sacrifice to God, counting you the offscouring of all things (1Co 4:23). Moreover, S. Augustine (in loc) thinks that this was said to console the Apostles. The Jews will cast you out, but I will gather you, and ye will convert so vast a multitude of men to Me, that the Jews, fearing the desertion of the Temple and the Law, would kill you, considering that they would thus greatly honour God, by killing you in their defence. The martyrs of Lyons considered that this was fulfilled in their case (see Euseb. v. i.), quoting this very text.

Christ here foretells the persecutions of the Roman Emperors for three hundred years, in which more than 200,000 Christians were martyred. They were led to this by various motives. As though fearing the destruction of their empire which rested in their hereditary religion. As regarding with abhorrence the worship of a crucified man which the Apostles taught. As seeing their own vices and impurities uprooted by the Apostles. As persuaded by their priests that the Christian religion was the cause of all public calamities.