"Everything” or “all things” refers to all our sufferings and trials, persecutions, calamities to which we are exposed. Paul has in mind the sufferings of believers.
Paul does not say this promise is true for everyone. He clarifies it by saying God does it for those who love Him and are called according to His purpose. It is true only of those who love Him. What is that purpose God has in mind? His goal is that we be conformed to the likeness of His Son. This is not a promise that “all things” work together for all people everywhere.