Why is obvious: to make the story better.
To unpack that a little:
Parents are characters, and all characters who don't pull their own weight for story purposes ought to be cut. This is why they often don't have siblings, either.
Furthermore, if not actively evil, parents are resources. (Which is why keeping an evil parent or stepparent around is a lot commoner than helpful ones.) Resources limit the writer's ability to plunge the hero into deep, dark trouble; therefore, writers wisely limit the characters' access to resources. Parents that aren't absent have to be neutralized somehow to let the hero shine, whether kidnapping or inability or purblind stupidity or what have you. If the parent is active, let alone both parents, the children will naturally tend to be demoted to sidekick. (What sort of good parent would let the child be centerstage for the danger when he could take on that role himself?)
Well-meaning parents who are not supportive are another form of conflict, to be sure, but not suitable for all stories. If they are the sole opposition, it's hard to play up their well-meaning too far without its being negated by stupidity (they are stupid, aren't they? You aren't sending your hero on a wild-good chase?) and as another faction, they need to be removed or assilimiated into the main factions by story's end.
Nothing gets to be a cliche without good reason.