Religious Freedom or Criminal Activity? Which is it?

I was just searching the Internet looking for a middle-eastern nativity scene for purchase.  In that search I came across a brief article about a human-sized "political" nativity scene that was vandalized at a church.  I thought this a bit strange, and realized that a Christian could be charged with vandalizing a Christian nativity scene, because they considered it sacrilegious, but if a Muslim stole an image of Muhammad, because they found it offensive, it might be considered practicing religious freedom. In our society, to some degree certain religious beliefs and commitments are idolized, whereas others are scrutinized - and not with the same measure.  In this fictional scenario, the media and protestors would be up in arms advocating for the Muslim who rightfully was defending Mohammad, and would also be up in arms in opposition to the Christian who was defending Jesus.  At the same time, in other parts of our country, the Muslim would not even have a chance to explain himself/herself before being carted away to jail, while the Christian would be championed and put up on a pedestal.

This article also made me concerned about how expressing one's opinion against homosexuality is starting to be considered a hate crime. What happened to true freedom of speech?  I am concerned about hate crimes - a person's life and property should not be endangered because of their sexual orientation.  But, when a person can no longer express their beliefs with strength of emotion in a public setting, then we are all in trouble.  I emphasize "public setting," because I also think it is inappropriate to use a funeral - which is a private event - as a place for staging political and religious commentary that is different than or critical of the deceased's views, beliefs, values, and profession.

This is all to say, where do we draw the line between religious freedom and criminal activity?  How do we protect the individual from harm  - the harm of losing the right to believe as s/he wants and - the harm of having violence directed at you? Do we truly defend the right for all to believe and express what they want to believe or does society choose certain beliefs as acceptable and others as unacceptable?  If so, how far do we go with this?  What is our boundary line? and What is the basis of that boundary line?