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Not sure why that would be confusing. Cersei controls the Kings guard, and used this cult to do her bidding separating herself from directly being involved in these matters. The King could take control but he is weak and young and easily manipulated by his mother. So with Cersei controlling essentially the police of the city, the cult has been allowed to run rampant to destroy her enemies. But it turns out that leader is actually true to his beliefs as far as we can tell, so even Cersei is not safe from them.
So now crazy cult has all the power, unless Tommen can put on his big boy pants.
I am not a fan of this particular storyline, but it makes sense and they did a good job setting it up.
Where exactly were these militants before all this though?
Do they outnumber the guard loyal to the lannisters? Who follows them? All poor people?