Religion in of itself only consists of ideas, ideologies and beliefs. To say that religion is a major part of discrimination is therefore in my opinion an oversimplification of the nature of discrimination.
Consider that there are people of various religious views who retain the ability to value and respect those who differ from themselves. However when discrimination becomes and issue in a religious arena you don't hear about the respectful people, but rather the extreme outer spectrum of that religion.
People have a nasty tendency of lumping a group together when one crazy member of that group does something negative. That has nothing to do With religion and more to do with the self defence mechanisms people develop when they perceive something as a threat.
I also believe that the media is a major contributor in causing many people distress and negative feelings towards religion as whole. I'm not saying the media is anti religion, but listening to the news we hear a lot about the horrible things going on in the world. For instance with ISIS who are killing anyone who do not agree with them. They are a good example of a poor representation of a religion.
If I were to point to what I see as the major culprit of discrimination I'd say it is a combination of blind ignorance and a lack of proper education. Specifically being educated in critical thinking, psychology and sociology. If you've never been taught to listen to a differing view than your own without blowing a gasket it is a good indicator that you are prone to discriminate against others as well.
So in conclusion I'd say that it is too simple to say that religion is a major part of discrimination. Because at the base of any type of discrimination there is a layer of ignorance, an uneducated mind and fear. The thing about those denominators is that they include people inside and outside of religion. Religion doesn't even have to be a topic for discrimination to occur. The subject of discrimination is so multifaceted that it would be impossible to write down absolutely every aspect of it. It is a fascinating subject though.