Okay, firstly, the film rights, TV rights and comic rights are all different.
There is nothing wrong with the characters co-existing in the comics, Wolverine, Cap, Spider-man, etc. These are all owned by Marvel comics.
They have always been there. That may never change anytime soon. Since they are all owned by Marvin Comics, each of the crossover can happen or has happened since the creation of each character (Spider-Man, the Avengers, the Human Torch, and Namor).
Coming to TV rights, all the rights to all Marvel's characters were bought by Disney, which can be used just as they are being used in the comics. For instance, Hulk has teamed up with Spider-Man in XD's Ultimate Spider-Man cartoon and can still do so any day. As far as these animated TV films are concerned, it is right to assume that Disney now has absolute control over the characters as well, just like Lionsgate did before them. This goes on to prove that Disney will be allowed to do a Civil War TV movie whenever they feel like doing so.
Now enters the film rights. This is where most people get confused the most. Several years ago, most of Marvel Comics sold off several of their character's rights to different recording studios, like Fox, Universal, and Sony. Because the Spider-Man and X-Men films were unbelievably successful, Marvel Comics opened their film studio known as Marvel Studios. Recently, Marvel Studios got their film rights to Captain America, Iron Man, and Thor. These were previously owned solely by Artisan, though they never did anything meaningful with them, so Marvel had to get them back. They equally re-obtained Namor and Hulk, who previously were under the name, Universal Studios. With these unique characters returned to the control of Marvel Studios, it becomes possible and easy, not only to produce and Iron Man movie, but also to have Iron Man, Thor and Hulk in one film, without anyone getting a law suit. Now that was great. The dream, however, became a reality when in 2012, an honest to God Avenger film that does not suck was produced.
It wasn't possible for Marvel Studios to retrieve all their rights with works like Spider-Man and X-Men doing so well at Sony and Fox respectively. Sony and Fox wouldn't dream of giving up the rights to these works for anything in the world. If Spider-Man ever meet Captain America in the Avengers movie, Marvel and Disney would be sued to their last dime because he has become Sony's property.
There are, however, some exceptions here. For instance, the characters Scarlet Witch and Quicksilver were members of the Avengers for a long time and also belonged to the X-Men, which means they can be used by both Marvel and Disney. Though they never say why, but they are prohibited from discussing mutants, Magneto or the X-Men. While in an X-Men movie, they are never allowed to talk about the Avengers, Iron Man, or Hulk.
If after several years, Fox fails to make a movie without any of these guys, the rights naturally go back to Marvel. Fox cares about the huge financial worth and potentials of these characters and won't let them go until people stop paying to see them. This was exactly what happened with the Punisher.