I remember in the 1960's there were many political philosophers who argued that the state tolerated opposition provided that it was ultimately not going to threaten the status quo. When liberals complimented their society for its freedom those opposed to them would say that the freedom only extended as far as allowing non-revolutionary change. In fact the latter sometimes suggested that the toleration of opposition was repressive, since it directed what would otherwise be radical demands for change into something more amenable to social cohesion.
Whatever one thinks of such a theory, the idea that people should be free to say absolutely anything at all has recently been challenged by the Charlie Hebdo events, and in many countries there is legislation forbidding people from saying things that are held to be offensive by others since that might lead to violence. Are we not entitled to demand a level of respect for other people and their beliefs? If I have a Jewish neighbor and I greet him each morning by calling him a fat Jewish pig, am I expressing a view which should be protected or am I being needlessly offensive? Perhaps this should not count as political speech, but if I abuse through speech or print the government in Turkey a recent law would punish me, and that seems to be going too far. A problem with encouraging violence is that it threatens to undermine the possibility of people living together amicably in any sort of society.
There used to be a saying in England that in a free society you can do anything you like so long as it does not frighten the horses. As you suggest, this implies tolerance for what is unlikely to upset the existing system, but those opposed to you would see violence as something that not only overthrows a particular government and sets up the conditions to continue to do this, to the detriment of society at large. Hence there might be grounds for disallowing it.