He has directly assaulted the free exercise of religion by defining the exercise of religion as the rituals that happen inside a church.
He has spoken out against free speech when, in particular, he said that "The future must not belong to those who slander the Prophet of Islam" rather than "The future must not belong to those who commit violence to advance a political agenda."
While he has not done anything overt against the right to keep and bear arms that I recall, he has a record of disagreeing with that right. (And it is possible that Fast and Furious was an attempt to justify gun regulation.)
He has spoken out against the right and duty of states to legislate all matters not reserved to the central government or prohibited..