My charitable guess is that Content ID isn't available to everyone because of scaling issues with the vetting process for the database. While it's theoretically possible to open the floodgates to everyone, that would present a massive human resource challenge for Google. I have no idea how Google's vetting process works for those who meet the eligibility requirements...but I imagine it involves lawyers and background checks to verify that the ostensible copyright owner is who they say they are, and is indeed the owner of what they claim to own.
Setting a high bar for eligibility presumably cuts down on fraud, wasted cycles vetting obvious noise, and the need for an army of people to do the vetting and legal checksumming around the clock.
The little guy is collateral damage in this case, not the intended target. You could argue, hey, potato potahto, the net result is a system that favors the large content publisher and offers the little guy no chance to participate. But intent matters. If Google's intent is to manage scale, then hopefully Google acknowledges the unintended problems its solution creates, and it's working on a better solution. If Google's intent is indeed to favor the big publishers, then that's a different story.