Amazon isn't trying to cut out the middle-person. Amazon is trying to MONETISE the middle-person. It is doing this by (it seems*) pushing to charge for publisher perks, such as pre-orders, personalised recommendations, and for having a dedicated Hatchette representative working at Amazon (a Hatchette Account Manager (HAM), if you will). Reference is here: http://the-digital-reader.com/2014/06/21/new-leak-reveals-amazon-wants-increased-co-op-fees-hachette/
Amazon believes in the long tail and is quite content to leave indie writers alone for as long as it makes sense for it to do so. (Yes, Amazon may well screw over indie writers in the future but, here and now, that's not what's happening.) What YouTube is doing is completely different, going after indies proactively by penalising them while offering better terms to the large recording companies on the same platform.
The only similarity is that Amazon is big and YouTube is big. Other than that, the two are playing completely different games. I agree about finding indie music, though. It's a lot tougher, but ultimately more satisfying, than listening to the dross that currently passes as Top Twenty "music".
* I say "it seems" because, as Nate Hoffelder points out (link above), all the leaks so far have come from Hatchette, and we know that a company will never knowingly "leak" information detrimental to its own position.