The punctuation tradition tells a story about a conjunction "потому что" (preceded by comma by usual reasons) and pronominal adverb "потому" which can be modified by a subordinate clause with "что" (but can also be used independently - same way as determinative pronouns such as "тот" can - "Тот человек, что вошёл сюда").
The variant with comma in between is definitely preferred when there is a modifier like "только" which seems to be related to 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 explanation along the same lines) is allowed for "несмотря на то(,) что", "для того(,) чтобы" and several others. It is not clear whether there is a limited list for "omit the comma" (though "потому что" seems one of the most robust cases) or it is enough to be anything that contains the "тот" pronoun etymologically and can be replaced by a single word ("ибо", "хотя" and "чтобы" respectively for the cases above).