The non-commercial content on YouTube is decidedly not the content which is protected with the copy-protection which the RIAA is (presumably) alleging that youtube-dl circumvents.
It's frustrating because the RIAA is not just requesting that the "infringing" part of the tool is removed. They want the entire tool removed, even for the parts which there is no question of infringement. For example, the 100's of other websites that it works with.
