Jyothi is the flame tip or the light, where as aatma is the soul. So, the supreme diety called as the SHIVA was ascribed the Shape of Jyothi or Aatma. Hence if you go to the holy places of "Chidambaram", "Srikalahasthi", "Ujjain",Rameswaram","Kedareshwaram".... you will find that they are called as the "Jyothirlingam". They are in no way the human reproductive organ. In Gokarnam, on the west coast of India, you will find the "Aatma Lingam", this is slightly different in shape, as it represents the Aatma or the soul. There are numerous places of Shiva worship like Mahanandi, Yaganti, Srikalahasti, Brihadreeswara and in kanchi, etc where you will find the Lingam being worshipped, which is infact the representation of the Divine. The stone is not divine, but one of the basis of Hinduism is that Creator is omnipresent. So, people over the generations, believe in the concept of praying for the idols, and they are expressing their devotion to the God that is present in that form and not to the material stone.
Nandi, the bull is depicted facing the sanctum in all Saivite temples, symbolizing the human soul Jeevatma yearning for realizing its oneness with Paramatma, the ultimate reality.
