No, it's true. My father is an author and my wife was book seller for years, so I've seen the publishing industry change close to first hand for about 20 years now (before that I was too young to really grasp it). There was a time not long ago when publishers would take a gamble on a new author or a really innovative work, fully expecting that most of the time they'd take a loss on the project, because occasionally they'd get something really good out of it. That, and the publishing world used to more or less be run by people who were enthusiastic about literature, and so would take a gamble just because it was something they liked or felt was important and worthy of publication. More recently, most of the larger publishing companies have been bought out by parent companies, and they do business the same way everyone else does: lowest risk for highest reward.
So if you can publish a book by a new author with a new idea, or one who's written something in a genre that's really hot right now, what are you going to do?
The old publishing world might well publish the author with the new idea because someone really likes the book or thinks it might really get a lot of attention. The current publishing world would tend to choose the hot genre. Both probably have the same potential reward; either could become a mega hit (in all honesty, the new idea might be bigger because people might get sick of the hot genre and want something new), but you know the hot genre is going to, at a minimum, make a return on investment while the new idea is a gamble. You might take a loss.
That being said, Jimbunny is right, this isn't really that big of a deal. Publishing has gone threw similar periods before and there is always some room for the truly innovative books; if nothing else, publishers always keep a few slots open for books that could win literary prizes, and "I'm a vampire in love with a werewolf who's also a witch" isn't going to win the Newberry award these days.
The thing to focus on is that kids are reading, and they're reading things they choose for themselves. I'm willing to say that I think Twilight itself is upsetting because it has some really creepy gender politics and because I'm a little offended that she used the name of a real Native American culture but then steadfastly refused to do any research into that culture. But I'm not sure that's true of everything in this genre.