I don't really get why these companies feel like they are getting cheated out of profit. It's not like they are putting up their own videos for monetary purposes, and getting cut out of it. If no YouTube videos existed of people playing it, it's not as if they suddenly would be making more money from YouTube. So then, the only argument is that they believe that people are not paying for the games, and would rather watch people play it. But that's just silly.
While I know not all videos are being taken down, and are instead just being flagged, it's still really shitty/petty.