There are crimes motivated by hate. These crimes unfortunately tend to enjoy a certain amount of covert support from the community (perhaps this is what defines a hate crime?), so it was decided that we should punish them more harshly in order to counteract the idea that they're somehow really okay.
It seems to me that this is a kluge; what needs to be fixed is the system which allows perpetrators to go unpunished (or minimally punished) when the crime has covert support... or at least we need to have a clearer understanding of what a "hate crime" really is, and why it has special standing.
I started to write "a murder should have the same penalty regardless of whether it's black-on-black, white-on-black, Christian-on-gay, Muslim-on-apostate, or whatever", but there are probably circumstances which should be taken into account.
The situation is complicated a great deal by the fact that we have a lot of bad laws which should not be universally applied, and by the fact that law (at least in the Western tradition) is something of a blunt instrument by which to enforce moral behavior.
More on this as time permits, but comments are welcome.