Partly because it's not Apartheid. The only state that is anything nearly as bananas legally as Apartheid* is Israel, and the Israelis actually allow quite a bit of inter-communal contact if you were lucky enough to be on their side of the border after the war of '48. The tricky bits come in the Occupied territories, where the Israelis make an argument that works fine for a few years. If you're militarily occupying another country you do get to run things, and they don't get to vote, but OTOH if it's lasting 50 years and you still can't/won't create a puppet government to govern things like zoning and water rights it's kinda hard to believe that you're actually doing this shit because you have to.
In Malaysia it really isn't apartheid in any meaningful sense of the term, because they don't stop all Chinese or Indians from doing much of anything. A Chinese kid can get into any university save one. He can (in theory) get almost any job. He is just much less likely to pull that shit off then a similarly qualified Malay, because Malaysian Affirmative Action works exactly like Conservatives think American Affirmative Action works. The other major issue for religious minorities is that the islamic Courts can be remarkably dickish. One renowned ethnic Indian athlete was declared Muslim on his death, so his family could not have the Hindi funeral they wanted, apparently largely because one guy said he was a secret convert to Islam. In another case the Malay word for God ("Allah") was banned from Catholic publications, because it's also the Arabic for God and thus used in the Koran, despite the fact that the Catholic God and the Arabic God are the same guy (Jehovah or Yahweh).
None of which is particularly good, but considering the country to their North is engaging in routine coups d'tat to prevent the repeatedly-Democratically-elected Shinawatras, the entire region is working itself into circles to avoid providing homes to the Rohingya, the people who are implementing the Rohingya genocide in Rakhine state are also very iffy on democracy at home, etc. it's very hard for me to believe that it is true that we should make this particular problem the center-piece of our human rights policy for the region.
*The legal justification for Apartheid was technically non-racial, or as close to non-racial as you can get while setting up a real-life race-based caste system. The claim was that all black citizens of South Africa were actually citizens of their original tribe, that the Apartheid government had righted a great historical wrong by recognizing them as sovereign states, and that as citizens of their tribal Bantustan blacks were immigrants to the white bits (read: the bits people actually wanted) of the country and should be treated as such. Of course the "foreigner" had in most cases lived in the big city for multiple generations, probably couldn't even speak the tribal language (heck, even if you spoke Xhosa language fluently, and went to family reunions in Ciskei, the authorities were likely to make you a citizen of Bophutswana or something for obscure bureaucratic reasons).