Because of this, Marvel has started to phase out entire classifications of characters from the comic mainstream. For example, mutants (read: X-Men) are losing favor to Inhumans, a similar group of characters.
The Fantastic Four series, one of the longest running in comics, is ending shortly. Speculation is that it's because of Fox's ownership of the Fantastic Four film rights.
It's a slightly strong-arm tactic, but also in the best interest of Marvel's bottom line. Why publish comic books with characters that appear in movies that you don't own.
Had Sony not been hacked, they would likely still control Spider-Man.