Prophets, wise men, and scribes are the higher faculties sent up into a person's own awareness: the prophet the intuitive seeing that speaks ahead of the senses, the wise man the settled understanding, the scribe the ordering intelligence that records and interprets. That these are killed, crucified, and scourged is the lower nature putting to death its own finer powers whenever they threaten its comfort, the flesh silencing the very insight that would raise it. The persecution from city to city is this resistance driving those faculties from one center of thought to the next, giving them no place to rest inside the mind.
What happens is a self at war with its own higher gifts, striking down the messengers that rise within it. The rejection is internal: the crude self extinguishing the light it was meant to receive.
Prophets: the intuitive seeing within a person that speaks ahead of the senses
Wise men: the settled inner understanding that grasps the truth of things
Scribes: the ordering intelligence that records and interprets within the mind
Synagogues: the gathering places of thought inside the person, where the higher faculties are scourged
City: a fixed center of thought and habit the mind builds, one of many a person moves among