In the Chicago offices of US Catholic, a monthly magazine, the editor held an emergency meeting yesterday with her staff to discuss coverage of controversy. In New York, the editor of the biweekly Commonweal magazine arrived at his office to find a blunt e-mail message from a critic declaring, ''You're next." And at Boston College, the school's president was asked at a faculty lunch to explain whether the ability of professors to question teachings of the Roman Catholic Church is now under threat at the Jesuit university. The announcement Friday that the Rev. Thomas J. Reese, an oft-quoted commentator on...