Russia's crackdown on Jehovah's Witnesses is intended as a message that small ostensibly American religious sects that try to recruit others will not be tolerated in their country. So while it's heavy-handed and counterproductive, it is hardly the case that 'no one knows why'.
In addition to Russia's dislike of American sects, and the fact that JWs inherently will not endorse Russia's government, it is not entirely surprising that any government might perceive some JW views as 'extremist':
- 'Russia' is a 'beast' from Ezekiel and Revelation.
- All governments, including Russia's, will soon be destroyed
- Billions of people who refuse to accept their beliefs will soon be annihilated