Religions Role

[Gemm: Rock & Roll Star; Born to Rock]

Now, I'm going to have one province in my nation being ran by a religious group. What I'm wondering is how could someone come to loath religion? Could it be in how they are treated when they are around those that are the role models of the organization? I don't know how to answer this because I'm a very tolerant person.

I'll probably model it around Christianity, since I am of that faith, and know most about it.

[The Holy Saint, Grand High Poobah, Master of Monkeys, Ehlers]

I've seen a lot of people give various reasons to hate religion. Sometimes it's because they see one bad example and extrapolate that to all of religion. Sometimes it's because, as you said, they feel slighted by the leaders of the religion (said slight can be real or imagined). Sometimes it's because they just don't want to live it so they make up stories about how the religion misleads people. Sometimes it's because someone they know has said bad things about it (true or false) that they don't ever investigate for veracity.

[Lieutenant Kije]

If a characters fancies him/herself a "free thinker" you could have them buck against the dogma that organized religion often presents.  In fact the character doesn't really need to be an overt free thinker, they just have to question dogmatism.

It would be doubly effective if questionable acts/atrocities were committed in the name of that dogma (e.g. the Inquisition.)  

And especially doubly effective if those atrocities touched the character personally in some way (directly, through a loved one, etc.)