For me the difference comes when your disapproval/intolerance/hatred can be rationalised, and not simply based on name calling and ignorance. It is perfectly possible for the different denominations of Christianity to justify their existance relative to one another based on their interpretation of their Bible. The bigotry only enters into it when it's the mindless masses who don't even know what their own denomination stands for much less any other.
The same can be said for the attitude of Christians, Muslims, Jews, Hindus and Athiests etc to one another.