|I wouldn't mind to see shounen-ai inside of a "shounenish" story, a example of anime like that was NO.6, I remember reading in the MAL forums that a lot of people dropped it after
Spoiler (mouse over to view)
a kissing scene between Shion and Nezumi. But I don't really think NO.6 falls under "shounen-ai" either, but only seeing two protagonists doing that made some people dislike the anime... Since it is probably like BaeSooky said, "I read my shounen to get my shounen fix, and my shounen-ai to get my shounen-ai." So if you read a story that you don't even imagine two people being a couple, kissing etc, because it is out of character and only works good in djs (that somehow take the shounen feeling away), many would dislike reading shounen-ai scenes, even though they are okay with "gay love" in real life. There is also those who are totally against it too, be it fiction or real life, and would drop the manga/anime.
I think it is totally normal to be against a couple in a shounen manga and be okay with shounen-ai etc. It is like when I read yaoi manga, if I don't like where the story is going and don't want to see they together as a couple, it isn't because I'm against gay couples, but because I don't like that two characters as a couple. Same goes for those who don't like Luffy and Zoro, like you said, because you just don't like to see them as a couple. We have the same situation in both genres (shounen and yaoi), so I don't think it is homophobic to be against the idea of certain characters having a homosexual relationship in a shounen manga.
I don't know if I answered your question or just blabbed lots of non-related stuff.
TL;DR: there are those who are totally against "gay love" in real life of fiction, but also those who wouldn't like to see two characters from the same sex being lovey-dovey in shounen manga because it is out of character, "they don't have chemistry" or simply because it would lead the story to a unpleasant way.
:: myanimelist :: <3 ::