This rumor has been perpetuated on the 'Net ever since news that Marvel was cancelling the Fantastic Four comic book and also with the Death of Wolverine storyline, both of which happened last year. The rumor goes that Marvel is so dead set against doing anything to help Fox promote their Marvel film franchises that they were killing the ol' Canucklehead and cancelling the FF just to spite them. Folks, that is utterly ridiculous. First of all, the comics don't exist to promote the films, nor do they do anything at all to help the films succeed or fail. Quite the contrary, the films exist to promote the comics. To put it in plain English, there is absolutely nothing that Marvel can do in the comics that is going to have any effect whatsoever on the films. Marvel can't sabotage Fox, they simply aren't in that position.
Fantastic Four has never been anyone's favorite comic book (apologies to anyone who's favorite comic book is the FF, but you are in the minority). Pretty much since its creation, the Fantastic Four has been a struggling title. It has been through more revamps, reboots, rebrands and restarts than any other comic book in history. Marvel has spent the past 54 years trying to make the FF relevant, and the book has been hanging by a thread for dear life the entire time. To be quite honest, I'm surprised the Fantastic Four lasted this long. The simple truth is that Marvel didn't kill the Fantastic Four, the readership did. There have been memorable runs, to be sure, and those spurts have probably been the life support that has kept the book alive this long, but they would never have been able to sustain it, and that fact has finally caught up with them.
The first two Fantastic Four movies were, apart from the depiction of Doctor Doom, extremely true to the comic books. In fact, Doctor Doom was virtually the only thing changed in them, yet people still complained. The movies weren't at all badly written or directed, they are completely enjoyable and valid Fantastic Four movies. What people don't seem to realize is that if the FF movies aren't very good, it's because the source material isn't very good. Tim Story could only do the best he could with the tools he was given. The Fantastic Four failed on its own merits, Marvel didn't kill it.
The X-Men are a different story entirely. The X-Men got off to a rocky start, but have been a constant best seller for Marvel since the Claremont era back in the 70s, 80s and early 90s. All told, Chris Claremont wrote the X-Men for 18 years and I'm pretty sure that makes him the longest running writer who has ever written anything in comics. Claremont started a momentum that continues to this day, and the X-Men, another property whose movie rights are owned by Fox, is in no danger of disappearing, either from comic book racks or from movie screens. The fact that Marvel cancelled FF yet still retains X-Men should be proof right there that the decision to kill FF had nothing to do with the film rights. And this thing about Death of Wolverine being a move to strip the films of their star mutant is preposterous as well. First of all, killing Wolverine in the comics does nothing to the film character. Wolverine can be dead in the comics and still have a long life in the films. Second, Fox has already been looking to replace Wolverine, as Hugh Jackman has been saying for a couple of films now that he is getting too old to continue doing it. For now, it looks as though Channing Tatum's Gambit will be taking the reigns as the resident star X-Man in the near future, so if Marvel really thought killing a character in the books would hobble the films, they would kill Gambit.
The decision to kill Wolverine was purely a creative one. Outside of Jean Grey, Marvel doesn't really have the history of offing their characters on a whim like DC does. They have never really explored that territory with a big name heavy hitter like Wolverine. This is their equivalent of the Death of Superman. And while the character of Logan might be (temporarily) gone, the legacy of Wolverine lives on. Marvel has even launched an entire team dedicated to the legacy of the character and are calling it The Wolverines. Wolverine has been far from washed away in the Marvel Universe. He's still a major presence, even if in memory only for the time being. Please, folks, try and use a little common sense, would you please? Comic books don't live and die by the movies. Comics were here first and they will be here long after the movies have faded away.