When some of the animals do try to protest, Napoleon positions other animals to make some noise so that the protest cannot be heard. The animals are so dumb that they don't realize that they have just been silenced. Plus, the threat of the nine dogs instills enough fear that the animals do not want to stir them to have to defend Napoleon.
Later, Squealer, the media representative of Napoleon, uses fear to further persuade the animals not to make any protest of Napoleon's ideas. He assures them that if they do stray from the wisdom of Napoleon that Mr. Jones will return, this is certainly something they believe that they do not want.