The more things change the more they stay the same

Nearly 2000 years ago today the twelve "Scillitan Martyrs" were executed for their beliefs. Since then the world has changed in a very fundamental way more than once, yet people are still judged and persecuted because of their beliefs. Though it may seem like heresy to those who preach acceptance of all opinions, there are some beliefs that should not, that cannot be condoned. Where do you draw the line. When does something cross the line between that which (merely) makes you uncomfortable into something that is amoral by any standard of morality?