However when persecution is discussed in the Bible it is almost always in reference to the government being the perpetrators.
Wrong, the 'perpetrators' were always religious entities (almost always the Jews in the NT) oftentimes using/manipulating 'the government' and the masses as a means for their attacks.
Examples:
1 Now when morning was come, all
the chief priests and the elders of the people took counsel against Jesus to put him to death:
2 and they bound him, and led him away, and
delivered him up to Pilate the governor.
20 Now
the chief priests and the elders persuaded the multitudes that they should ask for Barabbas, and destroy Jesus. Mt 27
12 And when they were assembled with
the elders, and had taken counsel, they gave much money unto the soldiers,
13 saying, Say ye, His disciples came by night, and stole him away while we slept.
14 And
if this come to the governor`s ears, we will persuade him, and rid you of care. Mt 28
2 They shall put you out of the synagogues: yea,
the hour cometh, that whosoever killeth you shall think that he offereth service unto God. Jn 16
.....
ye by the hand of lawless men did crucify and slay Acts 2:23
1 But
Saul, yet breathing threatening and slaughter against the disciples of the Lord, went unto the
high priest,
2 and
asked of him letters to Damascus unto the synagogues, that if he found any that were of the Way, whether men or women, he might bring them bound to Jerusalem. Acts 9
23 And when many days were fulfilled,
the Jews took counsel together to kill him:
24 but their plot became known to Saul. And they watched the gates also day and night that they might kill him: Acts 9
50 But the Jews urged on the devout women of honorable estate, and the chief men of the city,
and stirred up a persecution against Paul and Barnabas, and cast them out of their borders. Acts 13
19 But
there came Jews thither from Antioch and Iconium: and having persuaded the multitudes, they stoned Paul, and dragged him out of the city, supposing that he was dead. Acts 14
5 But
the Jews, being moved with jealousy, took unto them certain vile fellows of the rabble, and gathering a crowd,
set the city on an uproar; and assaulting the house of Jason, they sought to bring them forth to the people.
13 But when
the Jews of Thessalonica had knowledge that the word of God was proclaimed of Paul at Beroea also, they came thither likewise,
stirring up and troubling the multitudes. Acts 17
12 But when Gallio was proconsul of Achaia,
the Jews with one accord rose up against Paul and
brought him before the judgment-seat, Acts 18
3 And when he had spent three months
there, and
a plot was laid against him by Jews as he was about to set sail for Syria, he determined to return through Macedonia.
19 serving the Lord with all lowliness of mind, and with tears, and with
trials which befell me by the plots of the Jews; Acts 20
11 And coming to us, and taking Paul`s girdle, he bound his own feet and hands, and said, Thus saith the Holy Spirit, So shall
the Jews at Jerusalem bind the man that owneth this girdle, and
shall deliver him into the hands of the Gentiles.
27 And when the seven days were almost completed,
the Jews from Asia, when they saw him in the temple,
stirred up all the multitude and laid hands on him, Acts 21
12 And when it was day,
the Jews banded together, and bound themselves under a curse, saying that they would neither eat nor drink
till they had killed Paul.
13 And they were more than forty that made this conspiracy. Acts 23
1 Festus therefore, having come into the province, after three days went up to Jerusalem from Caesarea.
2 And
the chief priests and the principal men of the Jews informed him against Paul; and they besought him,
3 asking a favor against him, that he would send for him to Jerusalem;
laying a plot to kill him on the way.
7 And when he was come,
the Jews that had come down from Jerusalem stood round about him,
bringing against him many and grievous charges which they could not prove;
24 And Festus saith, King Agrippa, and all men who are here present with us, ye behold this man, about whom all the multitude of
the Jews made suit to me, both at Jerusalem and here, crying
that he ought not to live any longer. Acts 25
17 And it came to pass, that after three days he called together those that were the chief of
the Jews: and when they were come together, he said unto them, I, brethren, though I had done nothing against the people, or the customs of our fathers, yet
was delivered prisoner from Jerusalem into the hands of the Romans:
18 who,
when they had examined me, desired to set me at liberty, because there was no cause of death in me.
19 But when
the Jews spake against it, I was constrained to appeal unto Caesar; not that I had aught whereof to accuse my nation. Acts 28
....and there's many many more....
Foxe's Book Of Martyrs, same thing. By far and away those killed were persecuted by 'the church', and most of those was over water baptism.
