I agree and acknowledge that homophobic violence is not limited to one religion or culture.
The article is about a specific culture with a specific religion and a specific set of laws - which I can neither support nor respect.
But to say "Islam does not seem to be the relevant variable here." is patently untrue based on the documented facts that they are living under Islamic laws. It certainly is a relevant variable. I suppose you would have a better argument if that was the ONLY issue with Sharia law, but it isn't.
Just like the Westboro Baptists "God Hates Fags" people are also hateful homophobes, but the fact they are using their Christian religion both as their reason and defense shows that their sect of Christianity is relevant to their views and actions.
Both examples don't condemn the other sects of their respective religions. Nor does it negate the fact that hate exists out side their religions.
Except that Sharia law and legal violence towards LGBT isn't unique to Indonesia, and their bases for both the law and punishment are based on the Quran.
I feel like your whole point is "You don't need to be religious to be a hateful homophobe." and I completely agree with that. In THIS instance of the article, the perpetrators do happen to be religious, hence my comment. I am confused by your comment that seems to want to deflect from the SPECIFIC issue here, though I would understand more if it was more of a broader, "It is a bigger issue than just this." Which I would agree with, and maybe that was your intent, but not how it reads to me. YMMV.