Why do the rest of the actors run off when Bottom reappears?

The events you are referring to take place in Act III, scene I of A Midsummer's Night Dream. When Bottom reappears, his head has been turned into that of an ass by the mischievous fairy Puck, who loves to play tricks. This startles Bottom's companions and they run away. Puck then aims to follow the other actors into the woods to frighten them even further by transforming into various scary forms, such as a headless bear, a hog a fire, and many others.  
Bottom does not know that he now has the head of a donkey. His companion Snout returns briefly and tells him that his head has been transformed, but Bottom takes this as an attempt to trick him and scare him. There is quite a play on the word "ass," which obviously has an ironic meaning. Bottom does not understand what Snout is trying to tell him and replies that Snout is acting like an ass–– when actually Bottom is the "real" ass! 

SNOUT: O bottom, thou art changed! What do I see on thee?
BOTTOM: What do you see? You see an ass head of your own, do you?

When Snout leaves, Bottom remains in the woods and starts to sing to prove his bravery, believing that his friends are only trying to make "an ass" of him. 

BOTTOM: I see their knavery: this is to make an ass of me, to fright me if they could. But I will not stir from this place, do what they can. I will walk up and down here and I will sing, that they shall hear I am not afraid.