First of all, these sites tend to shake out into two types. The first is pretty straightforward; people who just, for some reason, really don't like your brand, and are willing to spend $10 a year on a website to complain about it. The reasons are as diverse as people themselves. It could be they're opposed to your company philosophically for some reason. They could be a loyal fan of a competitor. They could be an employee you asked to leave who's still bitter over the situation.
These sites can hurt your feelings, but realistically, the only way they can seriously damage your brand is if they somehow become one of your top search results for your brand. And honestly, with intelligent reputation management, that's simple to prevent. You just need to ensure that positive news and fun discussion of your brand is shared widely and widely seen, and that will generally be all you need to put your "hate" sites well off your first page of results, where only those actively looking for them will find them.
And, really, ask yourself this: If they're looking for reasons to dislike you, do you really want their business? In the end, "hate" sites can only hurt your feelings, unless you let them do more damage.
The second type, however, is a little different and should be kept a close eye on; a website run by an activist group to specifically damage your brand. These sites are generally an outgrowth of other action engaged by this group; for example, it's not hard to imagine why People For The Ethical Treatment Of Animals is not a fan of most fast food restaurants.
These sites are often designed to try and hijack your search results, and you'll need to actively keep them from doing so. Or even better, just stop them in their tracks.
What Can You Do To Stop Them?
One way to stop these is pretty simple: Buy every variant you can think of negative domains. But that can get expensive, and honestly, if somebody is dedicated, they can find a way to get a negative domain.
Another effective method is to stay on top of your reviews and resolve situations where you can. Social media and email mean that you can reply quickly to negative reviews and customer complaints, and even do so publicly. Showing that you care about customers can often force even the nastiest critic to curb their bile, or risk being dismissed by their audience.
Finally, there's the tried and true method: using reputation management to make sure that your search results are more in your control. If you're making sure that positive, relevant news about your brand is out there, that creates a situation not even the angriest hate site can break through.