Half of taxpayer funded research will soon be available to the public

The short explanation goes like this: before Bayh-Dole patent rights were indeed with the federal government, but the Government did a rather poor job of turning the accumulated IP into money. Bayh-Dole was passed in the late Seventies, during the Carter-Reagan recession, and the idea was that the patents should now lie with researchers and universities because they would have a better idea how to exploit them, and it was unsaid that with this alternative funding channel open federal research expenditures could be reduced.

The long version is that it is really complicated. A whole new ecosystem has grown up around this environment, and the patent system as is is very suitable for actual commercial processes but not at all for basic methods used in processes.

Also: Stanford v. Roche

Wouldn't that mean that researchers would be less motivated ?

Here's another complication. Often, faculty need multiple sources of funding over the years to support their research, including federal grants, university support (direct through money or indirect through facilities and staff), and industrial support through gifts and grants. As well, the intellectual heavy-lifting is done by the faculty and their students.

If you believe in intellectual property rights, then who of all of these stakeholders deserves ownership of those rights?

Personally, I lean against faculty patenting their inventions. I'd rather the IP is open to the public. Even if a faculty member wants to commercialize their research, I think they are better off competing in the marketplace rather than through IP arsenals.

But, I understand the other point of view. Patent licensing is a lucrative source of revenue for universities (e.g., UFL and its Gatorade revenue) and inventors. As well, it's at least uncomfortable and perhaps unfair if opportunistic companies were able to commercialize on a faculty member's invention without renumeration or attribution.

Complicated topic.

As a well-known example, John Pople wrote a program called Gaussian while at Carnegie Mellon. Carnegie Mellon licensed the program to Gaussian Inc. When John Pople moved to Northwestern, he was banned from using the program he wrote, as was all of Northwestern University. Before the passage of Bayh-Dole, Gaussian was given out for free by Carnegie Mellon. Once Bayh-Dole gave them clear rights in the code, everything changed.

The physical medium is long gone, but for format is still the same - essentially non-interactive PDFs which emulate the paper.

Second, Publishers provide some value - they aggregate editors and peer reviewers, they provide copy editing and layout services, and yes, they produce actual physical copies of the journals.

These could be provided by other means, but most of those involve more work for the researcher. And after reading a vast swath of LaTeX layout papers, I value their layout services if nothing else.

Third, you seem to be assuming new companies aren't "disrupting the space". PLoS has been doing so for years, and PeerJ and eLife are picking up steam.

Any disruption would have to come from within academia, and it is coming because libraries simply cannot afford subscription packages any longer, especially packages from commercial publishers. Journals from scientific societies are less outrageously priced, although they are still bad.

Free access and copyright transfer aren't necessarily in opposition.