As an atheist I can acknowledge the wisdom of giving churches tax free status even though I don't want them to have special privileges. The concept is based on the ideal of separating church and state and requires something from the religion in exchange for their tax free status.
It amounts to this: Churches don't pay taxes and in exchange they don't get involved in politics.
President Bush (Jr.) actually had the IRS investigate a church because it was speaking out against the Iraq war. Meanwhile conservative churches, particularly in the South and Mid-west are politicizing with impunity.