For the most part, the initial cosmetic differences between major publishers and self-publishers are eroding, and consumers will not always have that visual cue that sets apart books by major publishers. As more famous and established authors turn away from major publishers and go independent, the line will blur even further.
This will cause more consumers to check out independent books that appear to be high quality on their face; and as they discover high quality and good reading on the inside, the impression that major publishers' products are always superior will further erode.
Eventually, there will be no strong indicator that one product is better than the other. Unfortunately, this trend could take decades to happen in the public consciousness, and all we can do is wait it out (and try to accelerate the process by presenting our own superior works to the public).