I agree with you. I do think people subconsciously identify Remus and Sirius as an unlikely couple because it is a same-sex one, but it’s a difficult thing to make people aware of, because most people will insist that they aren’t homophobic (they may not be, but they are probably heteronormative).
This is part of a problem in the way children are taught about prejudice. The lesson I think we all received is, “if you are prejudiced, you are a bad person.” People therefore respond to accusations of racism, homophobia, cultural appropriation, etc. by thinking to themselves, “bigots are bad people, and I am not a bad person, so I cannot be a bigot, there must be another explanation.” (This is an example of “cognitive dissonance,” I believe). What we should teach, of course, is that it is important to identify and address prejudice in ourselves, because it exists, it is negative, and it is probably there in some form.
So, R/S shippers, fighting the good fight since 1999.