Just because the church believes that something that prevents pregnancy is a de facto abortion doesn't mean that a secular government, which the US government is, no thanks to Republicans (sorry, couldn't resist), should tolerate or accept said nonsensical belief. While you can give abortion a pass, since it is legitimately a hot button issue, contraception simply isn't to the overwhelming majority of the rank and file. It's only controversial to the church leadership. They're free to believe what they want, but government shouldn't have to accept it as fact. Obama isn't telling you to go fuck yourselves, he's saying that he's not going to accept that what medical science says is not an abortion is an abortion on the churches say so.
Finally, as for the religious freedom argument, ask yourself this: if a Muslim group was asking for Sharia Law-based exemptions to US law, would you be as for it? I know I wouldn't.