How has the Church been persecuted throughout history?
Neh 4:7-11 Now it came about when Sanballat, Tobiah, the Arabs, the Ammonites, and the Ashdodites heard that the repair of the walls of Jerusalem went on, and that the breaches began to be closed, they were very angry. And all of them conspired together to come and fight against Jerusalem and to cause a disturbance in it. But we prayed to our God, and because of them we set up a guard against them day and night. Thus in Judah it was said, 'The strength of the burden bearers is failing, yet there is much rubbish; and we ourselves are unable to rebuild the wall.' And our enemies said, 'They will not know or see until we come among them, kill them, and put a stop to the work.'
Now in Nehemiah, the first thing to note is that none of the enemies are absent from this physical attack. While Sanballat is again at the front of the list, Tobiah and Geshem's people the Arabs are also mentioned. Sanballat is again the main orchestrator but he rarely seems to work alone. A brief look at the history of the Church shows us that Satan has used both of his friends in destroying and persecuting Gods people. In the first and second centuries the attack came from the Roman Empire, who frequently forced Christians to do lunch with lions. This is Satan using the world and its system (Geshem) to do what he ultimately wants. To "kill them and put a stop to the work." (vs 11) The Roman Empire became the Roman Catholic Church (Tobiah - that very "good" religious system who may say that Jehovah is good, but hates God's true people) and the persecution and deaths continued.
While in the west, we don't live in a country where physical persecution happens to anything like this extent, physical attacks and trials still come our way and are used by Satan to weaken our desire for God and the Christian life. In fact, it is the promise of God that "In this world you will have trouble". There, it's a promise! But our response to these trials is what God is looking for, and our faith is what He wants to refine.
From Nehemiah 4:7-15 Sanballat's Second Attack: Physical Persecution