It's pretty undeniable there's a Marvel deliberate editorial policy to shaft X-Men and push Inhumans in their place, and this comes from the movie wars.
However, there are a few things Marvel failed to consider:
1.) X-Men were too big to fail and still one of their best selling franchises
2.) Their replacement, the Inhumans, were handled horribly. First they take the 2 most popular characters (BB and Maximus) out of the book, then they kill off the 3rd most popular character (Karnak), then they introduce a bunch of new people nobody cared about. All to try and erase Inhuman history to make them more able to replace the X-Men niche, while simultaneously sabotaging them doing such. Combine that with delays and last minute changes and the attempted coup against the X-Men stood little chance.
Marvel has largely settled into the reality over the last 6-7 months that the X-Men are here to stay, imo. They've given up on replacing them, and Axis is testament to that. But there's limits on how much Marvel will tolerate, of course. It's why outside of Bendis (who is just doing his own thing) we're seeing unremarkable, unimportant, mostly Solo X-Books, with significant constraints on what new material they can create. The books are sidelined and rarely relevant to anything else in the MU. However that is not to say Disney has given up completely on their dream of erasing the X-Men to screw Fox. They are striking back, the whole "death of Wolverine" was a deliberate attempt to kill off the most profitable X-character both in the comics and in the films. It's why I predict Logan will not return under the comic book movie fad blows over.
Of course, the Fantastic Four were not like the X-Men and Marvel was able to get rid of them without major issue, replacing them partially with the Guardians of the Galaxy (whose book has become earth-centric sci-fi, former First Family territory).
In any regard to deny Marvel is deliberately working against X-Men and F4 these days comes off as delusional to me.
Or, for TL;DR:
No more needs to be said.