I watched the entire series on DVD in one big swallow (although I had to wait for S5 to come out on DVD but that's a different story), and had no exposure to fandom or anything. When I went to the web to find out what happened in S5, I nearly fainted dead on the ground to learn there were Brian/Michael shippers.
I agree with paraka who suggested it is a "slasher" phenomenon; I am not into slash, don't have any other fandoms, and find non-canonical pairings boring and totally uninteresting. The reason I LOVE Brian and Justin is we SAW them. I have no desire to see other guys, or women for that matter since I'm a dyke, from other shows have imaginary relationships and build a fandom around -- although I genuinely do not begrudge slashers their slashing! I'm just not one of them.
I also think that for fans who watched the show as it aired, in tiny drabbles with breaks between episodes and fandom discussions and no idea where the story was going, that you might get your heart set on certain things, and then have that color how you see the subsequent episodes. You might have spent weeks or months thinking something was going to happen, and then something ELSE happens, and it's hard to let go. I never had that experience with QAF. I got the whole story at once. I never lingered in doubt and speculation.
However, all that said, I knew in the pilot that Brian and Justin were the uber-couple: "And then HE came along." I saw Michael as having a painful infatuation with Brian and Brian manipulating that out of his own immaturity and need.
I do adore the Brian and Michael friendship and love Michael, which I guess is somewhat rare among passionate B/J shippers like me. But that's what my first, unspoiled, non-fandom but very obsessive discovery of QAF left me with.