My thought process is this:
Legal System is for protecting and maintaining a nation.
One large reason for prison to keep the "bad guys" for lack of a better term off the streets.
A person who commits a "Hate" crime is more dangerous to the community, and therefore deserves more punishment.
Here is why:
If I hate my mom. She calls me names, is a jerk to me, never encourages me, never lets me do anything, and I get soo infuriated with her that one day I shoot her and kill her, this is a horrible crime, it's murder. BUT, I killed my mom, and I don't want to kill anyone else.
But if I see another guy (this isn't the same person, this is an entirely new case), and he is a black man, and I belong to the KKK, I could go over their screaming White Power, and he could do nothing wrong, and I kill him. This is a "Hate" crime because I killed him specifically due to his race. This act is a lot more serious, because this man is willing to go to extremes against an entire race rather than one person like an abusing mother or a cheating wife. The threat to society is much greater and the crime itself is much more gruesome if it's fermented simply due to one's race rather than character.
While I do believe people call crimes "hate crimes" when they really aren't because of ones race, the merit and ideology I do believe in, and legit "hate" crime, at least in my opinion, deserves harsher punishment.