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It makes sense legally, but I've never understood why a company (or artist) would choose to remove a music video from a free distribution medium. After all, isn't the point of a music video to get more exposure for an artist, thus increasing his/her album sales? If this was a movie clip, it's a lot easier to justify because people explicitly pay to watch or buy movies... but not music videos.
Now, I know the super-techie-nerd will say that an individual could download the YouTube clip, and in turn get his/her own free copy of the song. But seriously... when I watch a music video on YouTube, I'm more likely to talk about the artist and send the clip out to my friends, which will create much more business value than stupid error messages.