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A hate crime is different than a simple murder or assault as it incites fear into a specific community. If a group of KKK members came into your community and lynched an African-American man this would incite fear among African-Americans. Similarly, if a Neo-Nazi spray paints a swastika on a synagogue this would incite fear into the Jewish community. An essential part of our judicial system is to ensure public safety and maintain public order. A hate crime affects more than just the one person who gets physically harmed -- it provokes fear into an entire community. That is the difference.
The only persuasive argument I've seen is given in the bill (Sec 2.2 and 2.5). Basically, if you attack someone because they belong to a specific group, you've also (negatively) affected that group. In any crime, those directly connected to the victim will be affected. If the crime is motivated due to hatred of a group, everyone in that group is affected, not just those with a direct connection to the victim. Since the effects are farther reaching, it makes sense to me that the crime would be considered more severe.