I'm sure I'll regret trying to impart some reason in this discussion, as I'm not a fan of Obamacare in any sense either, but Obamacare does not mandate that employers provide contraception. Obamacare mandates that companies with more than 50 employees must provide health care coverage of some kind for those employees. The government health care plan is only one option, and it happens to be accompanied by favorable tax incentives for those companies that choose to leverage it. That government plan is required to cover contraception.
Companies like Hobby Lobby are not required to take the government health care plan. They are highly incented to do so, but not required. They could shop for their own plan to includes the services and coverages that they wish to give their employees, and not the ones they have religious or moral objections to. And shoulder a heavier tax burden as a result, but that's because the point of a government program should be to leverage economies of scale - having an a la carte model where everyone can pick and choose what they want or don't want is not the most efficient and economical approach.
I find it ironic that the same people that will ***** that companies absolutely should be able to act like an individual in terms of having religious freedom are also the same people that want to ***** when companies make these same claims on individuals' rights to achieve things they don't agree with. If you put aside the religious aspect of this particular story, it's ludicrous to think that a company of any size has any "rights" comparable with a person, like freedom of religion or freedom of speech.