FWIW I don't think the status quo is ideal, the government should be getting more credit for and more value out of research that results in profit for private companies so it can invest in and lessen the tax burden of future research.
Tragedy of the Commons - Research into monitoring, maintaining, regulating, and improving resources shared by private companies
Positive externalities - Some research will not pencil out without including return on investment that cannot be captured by a company
Negative externalities - Companies won't invest in research to reduce injury to other parties (could fix with regulation also but depending on specifics this may be very difficult to enforce)