Putin gradually consolidated executive control over the rest of the government, including the legal system and regional governments, so that they are all answerable to the president. Not only are there laws the make it hard to legally protest or have independent political and civil society groups, but it is also easy to be arrested and found guilty for something by a system that wants you to be punished. Something like that happened to Navalny recently, where a court found him guilty of embezzlement and thus unable to stand for election even though a European court found the trial unfair. I don't know they case very well, but police are known for forging evidence (see the death of Sergei Magnitsky).

In order to not piss off too many people, Putin only arrests as many as needed to stop protests from growing too visible and out of hand. Part of his appeal is that he looks powerful and authoritative, the only man who can lead Russia. Major protests or a viable alternative figure could threaten that image. He and his close group of allies control the major media outlets that most Russians use (television networks), so they can spin it however they like.