Hate crimes are done out of malice for things that a person can't change about themselves. They are especially egregious and are needed to protect citizens that are more vulnerable to attack. All crimes are horrible, but murdering someone or beating them up for unchangable parts of who they are is especially troubling and disturbing.
The motives should not affect the sentencing. The existence of hate crimes only serves to perpetuate the belief that all humans are born into legally recognized societal groups, in direct violation of the United States Constitution, which clearly states that all humans are created equal and should be treated equally in a court of law. As stated by South Park, all motivations for a crime carry a degree of hate. If you kill another man of the same color, is it not because you hate that man? If you deface government property, is it not because of your hate for the government? The fact is, you have killed another man or defaced property and should be punished accordingly. The reason for commiting a crime should not affect the sentencing.
Punishing someone more for what would be a "hate crime", in short, devalues the lives of everyone who is not part of the group that is protected by such a law against the hate crime involved. For example, if someone is charged for a hate crime against someone who is gay, it would stand to reason that gay people are more valuable in society than someone who is not. By having a higher level of punishment, this is implied. In turn, it devalues everyone who is not gay. As someone who is gay, I personally just want to be treated equally... Not put on some sort of pedestal. Where's this whole "equal protection under the law"?