The essay touches on the reason for this phenomenon: if the kid is the protagonist, he or she can't have a parent around to take care of them, or they couldn't really "protag." But a further aspect of this that the essay doesn't really go into much is the writer's dilemma in accounting for the bad parenting. If the parent is truly bad— abusive, alcoholic, cruel, whatever— then the protagonist has to show some psychic damage from the effects. Gaiman and Stead solve the problem by making the parents merely pressed into less than optimal parenting by sheer economics. Both Miranda and Coraline are unequivocally loved and cherished, just not afforded much attention during office hours. J.K. Rowling, on the other hand, makes Harry Potter remarkably well adjusted for such a neglected child.
Another option in spec fic is to simply have the protagonist get plucked from the real world into faerie or an alternate universe, not because of any neglect but merely from circumstance. If Coraline were truly a YA protagonist of fifteen or sixteen, no one would consider her at all neglected. In fact, she would be unlikely to want to spend a lot of time with her parents. The essay also cites the Twilight series by Stephanie Meyer and lays a certain level of blame on Bella's mother for sending Bella off to live with her father so she can travel with her new husband, a professional baseball player. In fact, Twilight does rather succumb to what I call the Gilmore Girls syndrome, in which a teenager is somehow more mature than his or her parent(s). Not that Bella is a paragon of good sense, but Meyer doe make her rather maternal for her years.
And of course, spec fic can also provide dangerous situations that don't necessarily require the protagonist to have a run-in with a serial killer. Reading stories about kids in danger can be unbearably stressful. At the beginning of the Harry Potter series, Harry is an orphan, alone and friendless, but his dangers at the beginning of the book seem mostly those of emotional neglect. Rowling gives him friends, and then ups the ante over the course of the books, as things get more dangerous for Harry. She only really raises the specter or Harry's possible demise once the final book came out; by then everyone was thoroughly hooked.
So, in your favorite YA books, is the protagonist in danger? If so, where the heck are his or her parents?