Mariner:
1) There is considerable debate between the view of “freedom of religion” and “freedom from religion”; it is not as clear-cut as you would like to think. Regardless, even if it is “of religion,” the problem then becomes who decides what is a “religion”? Religious beliefs vary widely, even within religions. Practically speaking, freedom of religion becomes freedom from religion in certain circumstances, because we don’t want to get mired in the sticky question of what is a religion.
2) The bill of rights has been incorporated to the states through the 14th Amendment. Whether you agree with it or not, the courts treat it as such today, under the doctrine of stare decisis. There is also considerable debate over the true meaning of the 10th Amendment.