The difference is the peer review. If something is published in Nature, you can reasonably trust that it is legitimate science, and not a random person with no real credentials. Its an interesting cycle. People publish their best work in a prestigious journal because it is the most prestigious and trusted. Thus perpetuating what goes where. And this is also perpetuated by the grant system itself, you need to publish in prestigious journals to get grants to fund further research. You don't get funding to self publish on a university page. (I am not saying I think this is right, just stating the facts behind it)