The reasoning behind hate crimes is to speak as a society against targeting people because of some characteristic--race, religion, national origin, etc--that causes some people to become insensibly enraged.
Groups have been targeted for centuries, and as we saw in Armenia in 1915, or Rwanda in the 1970s, or Nazi Germany in the 30s and 40s, when group hatred gets coupled with power, attempts to exterminate may be not too far behind. We legislate against individual hate crimes to help act as a bulwark against that.
A hate crime is a reaction against that impulse driving the hater that thinks, "That person is ----. They have no right to existence. I can do what I want to them."
In our country, the hate crime statutes followed decades of unpunished lynchings, where authorities either turned the other way or were powerless to stop a community from acting on its collective hate.
To put it another way, try not to see it as, murder is bad but hate crimes are worse. See it as a reminder that we in society do not condone attitudes that foster hatred of vulnerable groups. It is also a reminder to those groups that they should not have to fear, that we in the majority remember our duty to protect those in the minority.
When society speaks against targeting people, it goes a long way toward stamping out virulent attitudes. Or at least it hopes to make people realize that they are not going to get treated more leniently because "it is just one of them".
And remember, contrary to what anti-hate crime decriers contend, we punish mental intent differently for similar acts all the time. Murder for financial gain, assault with intent to rape or kill, arson with fraudulent intent, breaking and entering with the intent to steal, etc.
