Marvel clearly doesn't hate the X-Men. It's a straw man argument made by Marvel to counter those who see the X-Men books less promoted, less licensed, less appearing as the face of Marvel Comics. Removed from T-shirts, posters, licensing, gaming, toys and much more.
This isn't a symptom of any Marvel hate, but the result of a decision, confirmed to me by senior Marvel staffers, that Marvel chooses to promote the characters that Marvel Studios controls, over and above other characters, even if a number of Marvel employees disagree with that position.
So, no, Marvel doesn't hate the X-Men. Marvel loves the X-Men. It's just that so do Fox Studios.
Still, if you did want some evidence that Marvel hates the X-Men… from this week's Hercules….
The Inhumans? Not the X-Men? When has anyone ever alerted the Inhumans to deal with a problem involving potentially invading gods? Hell, Hercules was even on a team with two X-Men and he definitely remembers…