Reason has an excellent article up about not only why the Hobby Lobby ruling was correct, but also why it didn’t go far enough. This part perfectly encapsulates the Libertarian argument:
A group of politicians cannot legitimately have the power to compel one group of people—employers, taxpayers, or insurers—to pay for things that another group wants. That's immoral, and it violates inalienable rights. Moreover, when government has the power to issue such commands—always backed by force, let us never forget—it sets off a mad interest-group scramble for control of the government machinery—because control is a license to steal. Is it any wonder that people are willing to spend billions of dollars to influence who makes government policy? If people face the alternative of controlling the government or being controlled by it, those who have resources will buy power and influence, even if only in self-defense.
Supporters of the Affordable Care Act (ACA) say the court decision permits the favored employers to make health-care decisions for women. No it doesn't. It only prohibits women, unfortunately in only a narrow set of cases, from being able to use government to force their employers to pay for those decisions. When did we start equating the right to buy contraceptives—which hardly anyone disputes—with the power to compel others to pay? It is demagogic to insist that prohibiting the latter violates the former.
Read the whole thing.