Putin prosecutes everyone who goes against him apart from allowing a minimal opposition to exist for the sake of appearance and venting off angry people's steam.
"Shut up, look down and you'll be allowed to live" is a very popular theme in Russia across all levels from the president down to local municipal offices. If you go against those in power you will be persecuted proportionally to their power.
The important thing to understand about modern Russia is that there is no separation of power. Putin owns the parliament, the government, the military, and the judges. As a corollary, everyone is guilty of something, and if not, they are made to be.