If they aren't threatening private property, or the safety of the police and public, you can't shoot them. They can be disruptive to a certain point - it's their right to protest.
There really IS no one answer. It depends on the situation at hand. Sometimes it is wrong to use harsh measures to control a protest, but on the other hand, sometimes it is the only appropriate response.
Yes it is wrong for the police to charge a crowd of peaceful protesters, but if said protesters aren't so peaceful, what are we to do? What do you want the police to do? Just give in? Surrender? Let the city be held to ransom by any group larger than 50 persons with a chanty slogan?
Protesters have rights, but so do the rest of us. By all means, let protests occur, but protesters cannot be violent or too disruptive. I'm sorry, but at least in my country we have this thing called democracy and a voting system. Let your voice be heard there. Don't go disrupting traffic or breaking windows just because you don't like something. If the majority don't like it, then it will be rectified in a democratic society.
Sometimes the police have no choice but to deploy "Crowd-controll" measures. I'm aware that these "less-lethal" methods can still cause grave injury and can even result in death, but again, are you going to let any marginally large group with a ideology do whatever the heck they want? Protesters don't always represent the people - in fact, in most cases, they only represent a particular group. Why they feel that their rights should supersede mine is a question I leave to them.