I'm seeing a lot of examples like this: Не потому, что я из россии, и не потому, что я организовываю.
I want to know the reason for having a comma between these words because I've asked a few natives, and they say that if I remove the comma, it would make no difference.
The reason is convention. Just as in English you could spell 'I' as 'i' and it would probably make no difference but the rules tell you to use 'I' because it is the conventional, the 'right' way.
In Russian, the convention is to set off subordinate clauses with commas. Потому is part of the main clause and что belongs to the subordinate clause, hence the comma in between. Notice that there is also a comma on the other side of the subordinate clause - before и in your example.
As a rule of thumb, putting a comma in front of что will be correct in 90% of cases. Many people do it automatically. There are cases though when no comma is needed. E.g. when two subordinate clauses are joined by и with no part of the main clause in between:
Notice no comma before the second что.
Punctuation tradition dictates that the conjunction "потому что" (preceded by comma for the usual reasons) and the pronominal adverb "потому", which can be modified by a subordinate clause with "что" (but can also be used independently - the same as a determinative pronouns such as "тот" can - "Тот человек, что вошёл сюда").
The variant with the comma in between is definitely preferred when there's a modifier like "только" which seems to go with the adverb part - "только потому, что" is better than ", только потому что" (and much better than the impossible "только, потому что").
This is additionally muddled, however, by the fact that the very same punctuational variation (with an explanation along the same lines) is allowed for "несмотря на то(,) что", "для того(,) чтобы" and several others. It isn't clear whether there's a limited list of forms that omit the comma (although "потому что" seems to be one of the most robust cases) nor it is enough to posit anything that contains the pronoun "тот" etymologically and can be replaced by a single word ("ибо", "хотя" and "чтобы" respectively for the cases above).
