Andover, a nearby town to Salem, has also been undergoing some witch trials. A lot of innocent people were in jail, and the townspeople were fed up with it. The townspeople in Andover were a step ahead of Salem in realizing that these people weren't witches, and that the courts were corrupted with power, illogical superstitions, and hysteria. So, in Andover, the people united and "overthrew the courts." They went to the courts and basically said, no more--you guys are wrong, and we won't listen to your authority any more. You have no power in our town. The people rebelled against the concept that the courts were always right, and had their best interest in mind, so they stepped up and kicked them out of town.
Parris, hearing these rumors, coupled with the fact that Abigail bailed town and that the people of Salem are growing discontent, is afraid that there will be rebellion in Salem too. Whereas he, the judges, Abigail and the other girls used to be revered in the town for their role in the accusations, the townspeople are angry now; in fact, he found a knife stuck in his door, a direct sign that the opinion of the town is turning against him and the courts. He is worried that the people of Salem, upset that their loved ones are in jail and that farms are going to waste, will hear the new that Andover rebelled against the courts, and get ideas into their heads that they should do the same. This would be disastrous for Parris--he has played such a huge role in the courts, that his job in the town, along with his reputation, would be ruined. He would be run out of town and have to start all over, with no money (since Abby stole his).
I hope that helps to clarify things a bit; good luck!