There is a strange idea in my head, I want to share it.

prolog

Currently we assume that Red John play with Jane his pervert games to have more fun by murding others. The classical reason for a high-level serial killer who wants a strong enemy.
There are a lot of movies or series like good vs. evil. (e.g. Homes vs. Moriaty) I don't think this series just use this old - in the past good working - pattern.

In my eyes, on this point we all were screwed. I think there is a big plot behind the scene. An organisation, which controls private companies and public institutions to rule behind the curtain, is the main bad guy at this show. This fits perfectly with symbolics and code words like "Tyger, Tyger". In our history there a lot of examples like that. (especially the use of christian methaphor)

I don't want to argue again the specific bible lines (apocalypse) or hints (like he is many), because in this board are a lot good explained theories. (please read them to accept that there is more than one bad guy)

main chapter 

Maybe I am totally wrong, but... What if this organisation identify Jane as potential risk for their "work"? He was a public man with a lot of intelligence. You can't kill someone like him easily. But an organisation of such a kind could keep him busy on another "focus". They make it personal to Jane and use Red John to murder his wife and daughter. (rage makes him blind and stubborn, at that point he got distracted)

You will doubt that Jane wouldn't be killed because he was public man. You are right. This is just on piece of the cake. In my opinion there must be a bond between at least on of the top guys with Jane. Currently, I don't know who could be this person. Maybe an unknown relative, an "old" pal of the past or an unreturned love. Red John knows a lot of Janes past. There must be a connection. (direct or indirect).

Why is he a risk? He had a public show at tv where he use his skills to manipulate people. He promise to solve the Red John case easily. Maybe the organisation worked already with Red John. Maybe solving the Red John case would lead to this organisation.

One last fact, that give me good feeling about my theory, is the following. The identity of Red John will be already revealed at the first part of the 6. season. Red John is just one guy (maybe just a tool) of the organisation. I don't think that all the future episodes after the revealing in the 6 season and the whole 7 season episodes will just tell us the story of Red John. I think Jane will hunt this organisation to bring them down.

epilogue
I know that my idea isn't waterproofed. But I don't think that my theory isn't too far of the truth.

Please, feel free to discuss this theory with me. :)

Before I forgot... imho... Ray Haffner fits perfectly Red John.