First, please note that it is not in Luke 19: 41-44 that Jesus is told to rebuke his disciples.  Instead, he is told to do so by the Pharisees in Luke 19: 39.  As to the gist of your question, Jesus is told to rebuke his disciples because they are acclaiming him as the king.

This story is from the point where Jesus is entering Jerusalem to begin the events that will lead to his death.  As he enters the city, he is being welcomed by his disciples and the crowd in general.  They are calling him the king and saying that he comes “in the name of the Lord.”  In short, they are saying that he is the Messiah.  This would have bothered the Pharisees who would have seen it as blasphemous.  They would not have believed that Jesus was the Messiah and would think it very improper for him to allow his disciples to say that he was.  It would be like how religious leaders would react today if a preacher were to allow his followers to say that he was God.