This is going to hit A LOT of people that upload to youtube. I have music turned off in FC4. Well that doesn't turn off some of the music in the cutscenes. What ever, that's fine. I'll just use the audio removal tool that youtube has. Here's the real problem though. That humming noise that plays when you pause the game, IS COPYRIGHTED BY MERLIN IDOL! That's absolutely ridiculous. I just got two streams I uploaded claimed by IDOL due to this reason. Both streams combined a total of near 6 hours. How do you turn off this damn menu "music"? Turning off music in the menu doesn't get rid of it. I play on pc. Where are the files to remove?
Have you looked at this thread that contains Ubisoft's policy on YouTube uploads of game stuff? It may offer helpful information or you might be able to get some help at the email contact listed there to overturn the copyright objections...
I don't upload myself so I'm not sure of the process, but it can't hurt to look.