I'll start this out by saying that I come from the position of a pretty strong free speech zealot. I'm a card-carrying ACLU member, and so on. But, there's a lot of confusion going on out there lately about what freedom of speech really is and means.
Free speech is a right of individuals and groups in relation to the state, not in relation to each other. This is something that the people who are kneejerking about the proposed or actual moderation of comments on web forums and blogs in response to the recent hateful and scary attacks on feminist bloggers should keep in mind. Allowing unfettered speech might be a good principle to try to uphold personally or as a community, but nobody has a right to be jerk or a bigot with impunity on anyone else's website or in any community's forum, any more than they have a right to spam someone else's site or forum. You delete spam, don't you? That's speech too, albeit often of a rather dadaist and puzzling variety.
And especially now that public outlets for anyone's speech are essentially free and fungible, even the principle of allowing unfettered speech is pretty weak. If someone wants to say hateful or bigoted things in relation to something I write, they can start up a blogspot blog for free and link/rant to their heart's content, and I can't and won't do anything to stop them unless they defame me or threaten me with violence. But I'm sure as hell not going to invite them to do it in my own sandbox that I'm paying for and maintaining and that carries my name and represents my identity to the larger world.
Reading this post at Slacktivist reminded me that these confusions about speech also extend to hate crime laws. The first big problem is a misapprehension of what hate crime laws actually do. Hate crime laws do not ban hateful speech. If they did, I would oppose them. The KKK and the Nazis can still have their marches and hand out their literature and run their websites, and I'll fully support their right to do so, though I'll also support my and everyone else's right to shout them down and/or ignore them. Again, they have the right to appear in the public square and say their piece without government interference, but the community has a right to express their opposition as well. If the community breaks other laws in trying to suppress their speech, such as by threatening or doing violence to them, then they're in the wrong, but vigorous opposition within the law is covered just as much under the 1st Amendment as the hateful speech being opposed.
As for the more nuanced issues regarding speech, thoughts, crime, and punishment: Hate crimes do indeed concern speech and thoughts, but only insofar as they pertain to motive, intent, and culpability for a crime. Consider the varying degrees of culpability involved in different scenarios in which a pedestrian is run down by a car: Someone who has a heart attack and runs down a pedestrian is less culpable than someone who accidentally does so, who is less culpable still than someone who is drunk and does so, who finally is less culpable than someone who makes and executes a plan to do so. As soon as you act on your thoughts to harm others, those thoughts become a part of the context and the evidence by which the nature of your crime and the degree of your guilt is measured, and it's hard to argue that the punishment is for some sort of "thoughtcrime," unless you think that either state of mind, thoughts, and speech should be inadmissable as evidence in any crime, or that everyone who thinks or expresses hateful or bigoted thoughts is inevitably going to act on them and should be preemptively charged.
So how is it any different to add another category to the above scenarios: someone who makes and executes a plan to run down a black man to send a message to others like him that they are not welcome or safe in a neighborhood, or to run down someone in front of an abortion clinic to scare others who might try to get an abortion? The murder is already a crime, and hate crime laws add in the possibility of an additional crime of attempting to terrorize a whole class of people, if said intent can be proven to the jury.
Something I don't quite get about conservatives who oppose hate crime laws is that they are often very much in favor of extra punishment for violence-as-speech when said violence is overtly political, which is called terrorism. Setting off a bomb and killing people is a crime already, so why add an extra punishment for the speech or intent part? That's the same logic as "assault is a crime already, so why add an extra punishment if the violence was intended to send a message to a particular minority?" And of course, it bleeds together at the margins. Was the KKK at the height of their power a domestic terrorist organization? I would say yes. They participated in and fomented violence intended to terrorize everyone else into accepting their preferred political and social arrangement. Their individual acts could be seen as hate crimes today, but when they became pervasive enough, it amounted to terrorism. When hate-motivated violence expands from individual cases to a broader social environment, it thus becomes political and pretty much indistinguishable from terrorism.
Now, there are some scenarios that are a little more exclusive to speech. You can probably be charged with a hate crime under some statutes for, say, burning a cross on a black family's yard. But, not all speech is protected. Credible threats of violence constitute assault under most assault laws (hence the distinction between assault and battery) and in the context of American racial violence, it is not hard to see a burning cross on your lawn as a credible threat of violence. In the very odd but I suppose possible case in which it wouldn't be, well, that's why we have prosecutors with leeway and jurys of our peers who have to be convinced beyond reasonable doubt.
So, to sum it up, speech is free, but not free as in beer, and lots of folks would do well to take that into account.