So it's self-contradictory to argue that things based on a choice deserve less protection than things that are inherent. Such a moral position is in itself a choice, and by your definition cannot be defended if e.g. someone inherently physically stronger than everyone else decides to go around smashing in the heads of people who believe as you do (regardless of your race or gender).
Religious intolerance is included because historically it has been one of the main reasons people have been persecuted and discriminated against. Heck, people are being executed for it right now in Syria and Iraq. Probably a lot more than because of their race or gender. Even atheism is a choice (essentially, a religion). The scientific method cannot prove a negative, so it cannot prove that a god does not exist. So to go from agnosticism (uncertainty about whether a diety exists) to atheism (certainty that no deity exists) requires a leap of faith - a choice.
If you boil it down, I think you'll agree that the key principle worth defending is the right to self determination - the freedom to make the choices you want to make. Such choices are worth protecting up to the point where they begin to interfere with other people's freedom to make their own choices. It's all about choices.