Andrew Dalke argues the philosophy of:
"If the public pays for the research, it should have access to the results of that research."
As being too vague, then provides supposed conflict on constitutional grounds:
"To promote the Progress of Science and useful Arts, by securing for limited Times to Authors and Inventors the exclusive Right to their respective Writings and Discoveries;"
- Article I, Section 8, Clause 8
Which is the constitutional basis for patents, not licenses.
For a patent to be issued, the code must be disclosed as well to demonstrate that is a unique idea or invention and it must in-turn identify prior art on which it is built.
Publishing code under an open-source or free license does not abridge the rights of the publisher (copyright still holds) or the patent holder (they can put limits on the license as the author himself notes with some proprietaty/educational licenses).
I think the real question is, as a taxpayer, why should I pay someone to develop a proprietary software tool which they can then make more money off of?