What I'll do is I'll go stanza by stanza, identifying the main message within each, and then look at how each ties together at the end.  

1. Lover divine and perfect Comrade, / Waiting content, invisible yet, but certain, / Be thou my God. 
   My lover and friend, who I have yet to meet, be my God. 
   
   
2. Thou, thou, the Ideal Man, / Fair, able, beautiful, content, and loving, / Complete in body and dilate in spirit, / Be thou my God. 
   You, perfect man, perfect in all ways, be my God. 
   
   
3. O Death, (for Life has served its turn,) / Opener and usher to the heavenly mansion, / Be thou my God. 
   Death, when life is done and I am ready for heaven, be my God. 
   
   
4. Aught, aught of mightiest, best I see, conceive, or know, / (To break the stagnant tie - thee thee to free, O soul,) / Be thou my God. 
   Anything that is mighty and superlative and lets my soul escape the mundane, be my God. 
   
   
5. All great ideas, the races' aspirations, / All heroisms, deeds of rapt enthusiasts, / Be ye my Gods.
   All things amazing, be my Gods. 
   
   
6. Or Time and Space, / Or shape of Earth divine and wondrous, / Or some fair shape I viewing, worship, / Or lustrous orb of sun or star by night, / By ye my Gods. 
   Time, space, Earth, beauty, sun, stars: be my Gods. 

Whitman's poem is fascinating because its refrain, "Be thou/ye my God(s)" is a command, not a query. He demands that everything in which he finds wonder, which ranges from mankind to nature to death to time, become like a deity to him. A 'god' is an entity that is powerful and is worshipped; Whitman is essentially commanding these things to become Godlike to him because he wants to worship them.