In "More on Academic Freedom and OA Funds," Stuart Shieber discusses whether subsidizing open access fees conflicts with academic freedom.
Here's an excerpt:
Kent says "libraries can't control the disbursement of open access fees precisely because of academic freedom." The premise here is that any method an OA fund uses to control disbursement must if effective necessarily cause a change in behavior of authors, for instance encouraging them to publish in less expensive journals over more expensive ones ceteris paribus. This much is true. Furthermore, there is an implicit assumption that any such policy that causes behavioral changes in where authors publish is coercive and a violation of academic freedom. They are not "free" to publish in any location because some are financially more attractive to them than others.
But no. Academic freedom means that faculty can study what they want, and publish the results where they want. It doesn't mean that the university must cover all costs for doing so, nor does it mean the university cannot cover some costs and not others in ways that redound to what the university sees as the benefit of its constituencies.