It's very nice of Obama to have occasionally acknowledged the existence of freethinkers in his speeches, but it doesn't mean much when his administration endorses blasphemy laws.
The public and private curtailment on religious criticism threatens religious and secular speakers alike. However, the fear is that, when speech becomes sacrilegious, only the religious will have true free speech. It is a danger that has become all the more real after the decision of the Obama administration to join in the effort to craft a new faith-based speech standard. It is now up to Congress and the public to be heard before the world leaves free speech with little more than a hope and a prayer.
Free speech doesn't mean you only have the right to say things that the majority agrees upon — it is also the right of a minority to offend the majority. I don't know why that is so hard to get across to some people.