The poorly thought out logic of this set of statements is hard to fully describe.
First of all, I defy you to find where in the United States Constitution your “thoughts” are protected. Your ability to speak ideas is protected to a limited extent, but not your thoughts in any degree.
Second of all, the First Amendment (neither directly, or through application via the Fourteenth Amendment’s due process clause) does not protect your right to encite criminal behavior. Thus, you could not stand on the street corner and say, “Go kill the fags, everyone” and have the “free speech” right protect you. So the very activity that would be punished more severely as a hate crime cannot be advocated with protection.
Which forces us to examine the idea of what in particular is being punished by hate crime statutes. What is being punished is not that you have an opinion that a particular group should be discriminated against. What is being punished is the decision to intentionally inflict a crime upon a person as a result of their status, where that status is specially protected. Thus, were I to go to a bar, tell everyone very loudly, “I think all Ay-rabs should get the fuck out of the country!” then head out and shortly after beat up a person whom I thought was Arab, if I have committed a “hate crime,” it’s not because I think Arabs should leave, or even because I don’t like Arabs. It’s because I selected an person to beat up on the basis that I thought they were Arabic.
Thus, you aren’t being punished extra for any thought process that, translated to speech, would be protected by the First Amendment.
Finally, the fact that we punish someone more for the fact they killed someone, for example, as a result of a “hate crime” doesn’t mean we devalue any other reason for killing someone. As has been pointed out in the excerpt from the opinion of the Supreme Court, the rationale for punishing the crime more harshly isn’t that we think killing someone for this reason is worse than killing someone for any other reason. Rather, we punish you more severely because we recognize that the action in the “hate crime” isn’t just bad because of what it does to the individual victim, but also because of what it does to our society. And in that thought process, yes, it’s worse to kill someone because you picked them out for being [fill in the blank with protected classification], rather than in order to take their $4. Similarly, it’s usually worse to kill someone because you were drunk behind the wheel, or because you used a more forbidden weapon, or because you were engaged in specific types of criminal enterprise, etc. Laws make that distinction all the time.
