Oh I know this song haha. 'que' simply means 'that' or 'because'.
In English it would be translated:
It's that me without you...
It's because me without you...and you without me...
The 'that' or 'because' in both English and Spanish implies that he is explaining/rationalizing his thoughts. It makes it more conversational. He asks the person he is singing to "tell me who can be happy......because of the aforementioned"
without the 'que' it translates as such:
It's me without you...you without me...
but this is simply stating a fact, there is no argument about whether they are together or not. You can even say that the use of 'que' can begin the sentence with "It's just that...me without you, you without me." (of course without the 'just')
I hope this helps. I used to live in latin America, and I'll go against most people by voicing that I believe Reggaeton is a great way to learn conversational, young Spanish...so keep it up. :)