There are several reasons why hate crimes should be punished more severely than crimes based on anger or revenge. First, crimes based on revenge or anger are understandable. I am not suggesting that crimes based on revenge or anger are acceptable, nor am I condoning these crimes. All I am stating is that these crimes are "reasonable" in a sense. Let me explain. If someone steals your money and hurts someone you love, you will be angry for certain. Now if you act on this anger and seek revenge by beating this person up and take his or her money in return, then it is understandable. In other words, I can see why a person would act this way.
When we come to hate crimes, there is little to understand. It is the height of foolishness to hate a certain category of people monolithically. People are individuals; not all people are the same.
Moreover, if hate crimes are not dealt with in a severe and swift fashion, the potential for greater crimes can be right around the corner. Think of genocide.
This is, of course, a matter of opinion. I do believe that there should be extra punishment for hate crimes because they are more likely to damage the entire basis of our society.
Other crimes are committed on a much more individual basis. A revenge crime, for example, is done specifically because of some problem between the two individuals involved. These crimes happen because of factors related to the indviduals involved. The idea that individuals could hate one another does not erode the very foundations of our society.
By contrast, hate crimes are motivated by ideas that do eat at the basis of our society. Our society is predicated on the idea that all people are equal. When you commit a crime that is done specifically because you do not believe that another group of people is equal to you, you are attacking the very basis of our society in a very serious way.
Therefore, hate crimes are more dangerous to our society as a whole than crimes that are motivated by more individual factors.