possibly a few reasons, if you want a certain bike,it may not come in a disc version, like my Look didn't. Also when you're going super spendy lightweight, a disc bike will (may) have to be beefed up/redesigned to handle discs, those few grams may be a deal breaker for mr weight weeny. Some people just maybe don't want or need discs for what they are doing. Often bike manufactures don't spec nice wheels with top end bikes as they assume you want the choice/have nice wheels, but either way, say you have a nice set of 2-3K wheels, what you don't really want is for them to be completely redundant from buying a new bike and then have to shell out $$$$ for new wheels...
I'll admit it took me a while to go disc on mtb partially cash related, but my first set, avid juicy's were OK but not that great, then my XT, took an age to get used to, and I can still live with some well set up V's... my first road bike, ultegra brakes/pads and DT swiss wheels... truly horrifying, well below acceptable braking in the dry, and scary as all shit in the wet. Going swiss stop pads helped but...ugh. New bike I went Mavic exalith (ultegra brakes), and they are truly astounding, wet or dry. Not as powerful as my XT mtb brakes (either set), but more consistent and better feel. If they made them form mtb i'd happily go without discs. But they don't
Don't get me wrong, I'm all for discs, they're geat, just putting forward ideas why someone might not buy a road bike with them.