I agree with paraka who suggested it is a "slasher" phenomenon; The fandom I'm in right now has this whole pairing that's pretty huge, and has a lot of fic just on it's own, but also plays secondary parts to a ton of other fics. And one of the characters spent a whole, oh, I don't know, 5 minutes on screen, where he chased after *plants*. If people can build entire relationships and undying love out of *plant chasing* than the subtext given in the M/B relationship is enough for people to overdose on. And hey *points to your icon* (I so need to upload some for IJ) Michael/Justin is my super secret QaF OTP. :P
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. Very true. Again with the current fandom I'm in, one half of my original OTP just *died*. I really didn't see that one coming. Also, bringing it back to QaF for some of the people who might have watched it from the beginning, they might have known/seen what happened in the UK version and assumed that since the US version was following (seriously have you *seen* the UK version? Some of the eps are almost word for word) and thought that Michael and Brian would be the main focus.
I actually find it amusing, especially since I've been in other fandoms, how seriously people in the QaF fandom take their ships. I mean I remember back when QaF was still airing (during the hiatus between season 4 and 5 was particularly bad) the epic ship wars that occured. In fact I created a group over on LJ, where people could discuss various ships *without* flame wars occuring, just because things were getting so crazy. I mean the fact that so far all the comments I've read, and even the OPs response to my original comment, all of them seem to be saying "Brian/Michael chemistry? What crack are *those* people smoking?" Not necessarily in a rude way, but in a *completely baffled way*. To tell the truth, *I'm* kind of baffled, because I don't see how people could *miss* it. I don't ship it, because I'm pretty sure Brian and Michael would suck together, and either end up killing or hurting each other, but I can't deny that it's there.
I do adore the Brian and Michael friendship and love Michael, which I guess is somewhat rare among passionate B/J shippers like me. Well thank god there's more than one. I *hate* when you go to read a nice little B/J fic, and you find out that the author has turned Michael into a psycho killer or something (I can't even *count* the number of times that has happened to me). I personally feel that Michael is the most misunderstood character of the show.