The reason for this was that Jefferson did not want to have his beliefs attacked and, perhaps, misrepresented by his political enemies. We know from looking at the way things are today that political partisans will use religion to smear their opponents. Imagine how much more Jefferson would have worried about this at a time when Americans were much more openly religious than they are today.
Jefferson was right to worry. When he ran for the presidency, one of the major attacks on him concerned his alleged atheism. His opponents claimed that he would do things like promoting the burning of Bibles and trying to destroy religion in general. Because he feared such things, Jefferson did not want his beliefs aired in public.