This is a strange prayer, for of course it was not the town's fault that the man was killed. The Chachamim generally agree that this is the community's way of denying responsibility for the murder, after all, there should have been at least one person in town who was willing to walk a little out of his way and escort the guest to his next destination to ensure his safety. So everyone is a little culpable for this man's death. We learn from this that we are all responsible, to a certain extent, for each other's well-being. This three-part ceremony is used to atone in part for the person's death, for each part parallels an attribute of the deceased.
Man is also like a tree which is always growing upwards and producing fruit.
The third component of a Human is his spiritual aspect.