This is a good question. Religious discrimination is a great topic and if you want to pick a theory to study this topic, you can use so many different ones. One of the greatest theorists of modern religion is Peter Berger and his social theories of knowledge is perfectly suited to study your topic.
He argues that all cultures have a commonsense worldview. So, what is accepted as true in one place is not necessarily accepted in another place. For example, in Saudi Arabia, monotheism is given. In the New York city, this is not accepted. Many people do not believe in the divine at all. In India, it is even more different, as the people in India are polytheistic.
In light of this, you can look at how social theories of knowledge lead to persecution. What can make this even more interesting is to look at secularism. Secularism can be even more intolerant than religion. Think of the former Soviet Union and China, two supposedly secular countries and their intolerance of religion.
Another possible perspective is to look at religion from a postmodern point of view. How does a relativistic postmodern framework view the many religions in the world? Furthermore, if postmodernism's theory that there are no absolutes is correct, then is it a defeating itself as it is making an absolute statement?