I think it's partly BS on the part of guitar players ("It's not a strat if it doesn't have 3 single coils"/"If you want a humbucker, buy a guitar designed for humbuckers... wait, what d'you mean the Les Paul originally had p90s?"/"The 80s sucked therefore everything even vaguely associated with the 80s must, too") and probably also the fact that some players don't like the big mismatch in output between humbuckers and singles. Not to mention that some players see them as "Jack of all trades" type guitars (to be fair, with some justification at times- if you have 15 different guitars you might not need a guitar that "does everything").
I like HSS a lot. I like HSH too. They're probably my favourite pickup layouts, if I only could have one guitar. I think they're both unfairly maligned, though at the same time I can understand some of the criticisms of them.