This is considered an important issue because of the two goals connected to it. The first is to protect government from the undue influence of the church. That is not to say that governments cannot be influenced by religious values, and it does not imply that we should become a secular society. That is not even a part of the discussion, nor should it be! But if you look back into the history of our country, you will find that churches strongly influenced the Salem Witch Trials. Elsewhere, you will find similar tragic results with the Spanish Inquisition, the Crusades and the Holy Roman Empire. That is not to say we are in imminent peril; it is simply to say that we should be aware that the seeds are there.
Similarly, the Catholic Church in the 1600s caused Galileo to be prosecuted for proposing the scientific belief that the Earth rotated around the sun. This is not an untypical response when churches have some controls over governments and governments attempt to question church dogma. The seeds are there as well for the suppression of such an inquiry.