1. It's different universities, including ones that don't directly fund research, and so more money in their pocket won't directly lead to more science funding. Also libraries.
2. There are many places to put extra money in a university (add to endowment, expand, etc).
>It would be more than fully outweighed because the universities would no longer have to pay the publishers the amount that constitutes the monopoly rent from the copyright.
Why do you think profit margins would go down? The "rent", to the extent a 30% margin is rent, is from the need to publish in prestigious journals. Copyright just affects how that rent is collected, but it's not clear to me how that would reduce the rent. (It may go down because people become more hesitant to publish due to the increased cost which forces them to lower their price to get more papers. But that wouldn't be such a good thing.)