I think that maybe Red John is not a member of Visualize, but he wants Jane to believe he is (maybe he even wants to mislead Jane into going after Bret Stiles specifically, either because he would obviously make such a good suspect, or maybe because Red John has some personal issues with Stiles and Visualize that he cannot solve by simply killing them).

I think that we just don't know why yet. Maybe Visualize (or Stiles) has taken some relative of Red John long ago, maybe Red John believes that Visualize is the only organization with enough power to compete with him and he wants to use Jane and the CBI to take them down, maybe he even has strong religious beliefs and wants to destroy Visualize for religious reasons. Or maybe Bret Stiles knows too much about him and has become a threat, some kind of threat that would be too dangerous to simply kill (imagine if Stiles has left a note somewhere in a safe to be opened after his death, revealing the identity of Red John...)