Army of Magus the Wicked
Full Name: Mystics
Symbolic Identity: Muslims
The Mystics, the long-standing arch-enemies of humans in Chrono Trigger, are in many ways similar to the role of the Muslims, followers of the Islam faith and historical rivals of Christianity.
Medina, the home of the Mystics of Chrono Trigger who fought an historical war with humans, holds a number of parallels to the real-life Middle-Eastern city of Medina, which is considered a holy city by Muslims.
Medina is, by Muslims, considered to be a divinely holy ground. The Koran specifically notes that impure, unholy peoples will be cast out of Medina. Notice that Medina Square is always a center of holy worship for the Mystics, where they worship either Magus or Ozzie as God. Indeed, it is a holy city to them. Also, notice that people who are not followers of Magus or Ozzie, such as Crono and his party, are quickly cast out of Medina as being the enemy.
The expulsion of Crono (Jesus) from Medina by the Mystics (Muslims) can also be interpreted as parallel to the fact that Muslims to not worship Jesus Christ as a diety, and reject Christianity as religion.
Now, one must also consider the fact that Muslims and Christians fought the series of bloody wars knows as the Crusades in the Middle Ages, over which many people to this day, Muslim or Christian, still hold a grudge. Now, look at the situation between the humans and the Mystics in Chrono Trigger: Humans (parallel to Christians) and Mystics (parallel to Muslims) fought a massive war in the Middle Ages (parallel to the Crusades) over which both participating parties still hold a grudge.
Elaborating on the parallel between the War of 400 A.D. and the Crusades, consider the fact that in both wars, not much is achieved aside from mass bloodshed by both sides. In Chrono Trigger, Magus and the Mystics never really succeed in taking over Guardia, the humans never really succeed in stopping them (recall that Magus and Crono's party all fall into a Gate after their battle, which stops the war), and countless people die during the war. Also, there was a Crusade known as the Children's Crusade, in which children and adolescants attempted to fight the Muslims (and wound up being sold into slavery before they got a chance to fight. In other words, they were completely innefectual). Similarly, notice that in Chrono Trigger, even a child, Tata, has attempted to take up arms against the Mystics (Muslims), and is completely ineffectual in doing so. Thanks to Sephiroth for info on what happened to the children of the Children's Crusade.