I think the general argument behind it is that the more outlandish elements of sci-fi are typically explained, whereas the elements and trappings of fantasy stories are relegated to the time-honored tradition of "it works because that's what it does".
For example; you can find entire technical manuals on any given model of the starship USS Enterprise of Star Trek fame. Warp mechanics and fuel issues are addressed realistically. Even the weaponry is commonly explained in real-world terms.
The world of, say, Harry Potter, on the other hand, leaves far more to the reader's imagination. Why do "wands choose the wizard", and to what degree are they sentient? How, exactly, does Apparition work, and what quality makes it traceable by the Ministry of Magic? Just how did the protective magic born out of the "power of love" save Harry's life and allow him to escape with only a scar?
When you mix the genres, you have some elements that are explained, and others that we're meant to take on faith. In fiction, that's something of a difficult hat trick to pull off.
Incidentally, the webcomic Gunnerkrigg Court [http://www.gunnerkrigg.com/index2.php] happens to deal with this very subject. The contrast between what can be explained by science and magic that simply works "because it works" is explored fairly well.
