The churchian abomination
They were persecuted because the Christian faith is the most radical re-thinking of the balance of power between Man, State, and God that has yet been posed. Instead of a religion preaching deference to the power of the State, Christianity teaches that there is a Power above the State, which answers to no instrument or organisation of Man.
Christianity is not about being tolerant and accepting of everything. Christianity is not about being welcoming to one and all. Christianity is never about submitting to violence and evil and hoping and praying that the Lord will simply deliver us from it without us having to lift a finger.