Rachel Maddow offers the best description of the hate crimes bill:
The concept behind this kind of legislation is often misconstrued but here's the deal as I understand it. The idea is that the federal Justice Department can get involved in a case to help local authorities or even to take the lead on a case if need be, in prosecuting individual serious violent crimes and murders in which the victim was selected on the basis of race, color, religion, national origin, sexual orientation, gender, gender identity, disability - the idea that crimes like that are intended not only to hurt or murder an individual, but to terrorize an entire community, and so there is a national interest in ensuring that those crimes are solved and prosecuted, particularly if local law enforcement doesn't want to because they are blinkered by the same prejudice that led to the crime in the first place.
While I appreciate the counterpoint that "a crime is a crime," imagine the complications surrounding the investigation of a murder and then compound those complications with a layer of bigotry -- whether from the community (from which a jury is selected), local law enforcement or the suspects themselves. It's impossible for justice to be served when the process is muddied -- blinkered -- by prejudice.