There are four primary differences between the two.
The first two are ones where I view profic as "superior" to fanfic. First off, fanfic is illegal and profic isn't. This is not an irrelevant concern -- we're talking about the theft of intellectual property. Does that mean fanfic shouldn't happen? Of course not -- I've written fanfic, read fanfic, enjoyed fanfic. But then, I also enjoy driving very fast, and sometimes state police have something to say about it, and I have to pay a ticket. Of course, most of the owners of those intellectual properties turn a blind eye, mainly because no money is being made off the fanfic, and since money is the primary reason for protecting your IP...
Secondly, profic has professional oversight. While it's true that there are good fanfic beta readers and that there are bad tie-in editors (and also bad tie-in editing jobs, which are often due to circumstances beyond anyone's control), in general, I'm going to trust the judgment of a professional in the field. Nine times out of ten, you'll get a better result from the pro than the amateur (which is why you generally hire plumbers to fix your toilet instead of doing it yourself). And way too much of the fanfic I have read is so obviously unedited it makes my teeth hurt -- and I'm not talking about typos and minor grammar mistakes, I'm talking about global writing problems that no pro editor worth her salt would let fly for half a second.
The third one -- and this and the fourth thing aren't value judgments in either direction, but simply stating the difference between the two -- is that fanfic is completely freeform. Profic has to be of a certain type: novel, novella, short story. These are formats with very specific needs and requirements. Fanfic writers, though, can go crazy. They can do drabbles, they can do scenes, they can do vignettes, they can do 600,000-word novels (some of them all one paragraph) without any complaints. Profic is much more standardized.
The last one, and this is the biggie, is that profic has to satisfy a much larger audience. There's really only one person who has to be satisfied with a piece of fanfic, and that's the writer. Fanfic writers are only obligated to be true to their own interpretations of the characters. And they aren't required to get a significant readership -- hell, most fanfics aren't read by more than a few dozen people.
Profic, OTOH, has to satisfy several people before it ever sees print: the writer, the book's editor, and whoever is responsible for approving the story, which in some cases can be several people (which goes back to the oversight thing above). That person approving the story for the copyright holder is sometimes someone intimately involved with the creation of the property -- and sometimes it's a flunky in the licensing department. But it's still a representative of the people responsible who has to say yes to it.
And there's another, far more important element to that: profic has to satisfy a much larger reading audience.
The audience for fanfic is, as I said, often a few dozen people. Some fandoms inspire fanfic to the degree that a few thousand people read it.
If that number of people bought tie-in novels, there would be no tie-in novels, because they wouldn't be commercially viable. The lowest selling tie-ins sell 20,000 copies in mass-market paperback, and most sell more than that. Fanfic's standards for success are almost nonexistent, and even their successes are miniscule in terms of numbers of readers compared to the requirements for mass-market publishing that have to be met.
What that means is that profic has to be palatable to a mass audience. The author's own unique interpretation, shared with several close friends, isn't really going to fly, because that singular vision won't necessarily appeal to a wider audience. (I'm not just talking about slash here, though that's the obvious, and there's no way a mass-market audience is going to go for, say Kirk/Spock hurt/comfort fiction.....)
So there you go. Hope this has been helpful. As likely as not, it's been inflammatory, but what the hell.....