Most of the time it is difficult to start charging for a service that was free for so long. Many users would feel cheated if that happened or they would feel that the owner of the company was greedy. If Mark Zuckerberg who is the founder and owner of Facebook started charging money for the use of Facebook Messenger, I think that many of the users would stop using it and would refuse to pay for it.
He may also lose regular Facebook customers due to doing that. However, there are so many other messenger systems besides the one for Facebook and these systems are free. People would just go to the other systems instead of paying for the service.