The ACA did not offer the same exemption to public, for-profit companies owned by religious people -- as well it shouldn't have. Just because the owner of a huge company like, say, Hobby Lobby, is an evangelical Christian, why should he be able to withhold contraception from those who work for him? The company's purpose isn’t to promote Christianity.
MORE: http://americanhumanist.org/news/details/2014-01-democratic-senators-atheists-and-churchstate-separat