According to the report, he has gone to the Eida Hachareidis offices and told them that he is giving in and will get the kashrut certificate for his store from the Eida or shut down entirely.

That is called protection money. Let's not forget, this store owner claims he only sells kosher phones and kosher certified filtered smartphones. The protests against him were for his unwillingness to adhere to the demands of local askanim (that he get the store certified with supervision, and maybe other demands). He is selling only kosher phones, but that is not good enough - the protests will only stop when he hires them to supervise his store. 

Might makes right and the police allow it to happen. Though the police are often guilty of the same - of might makes right, not of protection money, so maybe that is why they are ok with it.