The X-Men are one of the greatest teams in the history of the Marvel Universe. They faced and defeated foes that threatened not only their world but reality itself, and they accomplished that while being hated by a significant portion of humanity. Fortunately, many of the world's non mutant heroes support them and fight by their side. There are also non mutant heroes that support them begrudgingly, some even outright disliking them. It some cases it's because those heroes don't like The X-Men's method of operations. For others, it comes down to personal issue. In many cases, they just don't like Wolverine.
It's worth noting that Hulk isn't a big fan of most heroes or villains in the Marvel Universe but the X-Men are definitely on that list. His problems with them start with Wolverine, whose first comic book appearance was fighting the big green monster in the wilds of Canada. Their relationship never really improved after that. Hulk's bad vibes for Wolverine have generally extended to the X-Men as a whole, though he does fight by their side when need be. That being said, he'd be just as inclined to burn Professor X's mansion to the ground if the moment called for it.
9 Captain America
The Star Spangled Avenger doesn't have a problem with mutants. There was a point that his team consisted only of himself alongside Hawkeye, Quicksilver and Scarlet Witch. Cap has frequently been one of the first to come to the X-Men's defense when the situation warrants it. But he's also the first to stand up to them when he has concerns, such as the problems leading up to Avengers vs. X-Men.
Cap also took some issue with the X-Men staying on the sidelines during Civil War. He certainly respects their autonomy but also believes that the way they operate can do more harm than good at times.
8 The Thing
Yet another beef caused by the actions of Wolverine. Saying that Wolverine and The Thing have a tempestuous relationship is putting it mildly. It all came to a head when Wolverine attacked The Thing and slashed his face with his adamantium claws, doing damage that lingered for quite a long time. The injury was susceptible to attacks, making it necessary for Thing to wear a helmet. But considering Thing was already sensitive about his looks, this just exacerbated those bad feelings. They might be willing to work together now but The Thing understandably harbors a grudge that extends to the rest of the X-Men.
7 Iron Man
Wolverine isn't the only member of the X-Men that brings out strong feelings in the rest of the Marvel Universe. Namor has a tendency to do the same, particularly when it comes to founding members of the Avengers like Iron Man. They have faced each other numerous times over the years, even standing on opposite sides of the Civil War fight.
During the first Civil War, Iron Man was the one who met with the X-Men to make sure they wouldn't get involved. They agreed but their intolerance of his stance was apparent. The X-Men have about as much love for him as he does them.
6 Captain Marvel
Carol Danvers has a bit of an old grudge against a member of the X-Men, specifically Rogue. Her mutant power is ability to absorb the powers and memories of other heroes and mutants. This process can do a lot of damage, something Carol Danvers found out first hand. After an extended absence from the Marvel Universe, Carol returned but without her powers and a portion of her memories. This was due to an encounter with a young Rogue who still has the powers of flight, endurance and strength as a result. Years later, Captain Marvel is still angry with Rogue, something that colors all of her dealings with the X-Men.
It's entirely possible that the Punisher is incapable of liking or disliking anyone. He has a difficult relationship with Wolverine in particular but he's also not a huge fan of the X-Men as a whole. Frank's mission is one that has very few shades of grey in it. Unfortunately, those shades of grey are where the X-Men live their lives.
In the alternate reality of Punisher Kills The Marvel Universe, he slaughtered them for their role in his wife's death. While it's unlikely that the Punisher would ever outright go after the X-Men unless they found their way into his crosshairs in the main timeline, he has no love for them, either.
Wade Wilson is a difficult friend to have. Just ask Wolverine. While he as tried to join their ranks at times, Deadpool is one of the "heroes" in the Marvel Universe who finds the X-Men annoying. It pretty much comes down to how seriously the X-Men take...well, everything. Deadpool is a rather unstable individual who leans towards the side of the ludicrous whenever possible. The X-Men are a regimented group whose brand of fun is incongruous with Deadpool. Even when they let him hang around, it doesn't last long because he finds them insufferable.
3 Black Bolt
Not that he'll ever say anything about it but the X-Men drive Black Bolt nuts. As the leader of the Inhumans, Black Bolt knows what it means to be different in a world that doesn't accept you. They are essentially a species of mutants created by the Kree experimenting on humans a long time ago.
As much as you would think this might make them allies, it frequently put the two groups at odds. At one point, all out war broke out between the X-Men and the Inhumans. Black Bolt's silent rage towards the X-Men is something that will continue to fester and will inevitably lead to combat down the road.
A man of singular focus, Blade has spent much of his life hunting and killing vampires, attacking their systems and hierarchy to weaken them. He's also not above getting his hands dirty and running some stakes through some hearts. During the Curse of the Mutants, the X-Men asked for his assistance in dealing with a vampire problem. He and Cyclops had issues from moment one on how to deal with the situation. When Jubilee was turned, Blade wanted to exterminate her. Not surprisingly, the X-Men disagreed. Blade's one purpose in life is pretty straightforward and the X-Men got in the away of it. They won't be having a midday picnic any time soon.
1 Scarlet Witch
She seems like an odd name to include since she is a mutant but when you look at her actions from the outside, it all makes sense. Scarlet Witch has used her abilities to varying degrees of success against the X-Men. With three little words, the vast majority of mutants on Earth lost their powers. Few threats has had a greater impact on mutants than the Scarlet Witch, despite the fact she herself is a hero and a mutant. Her affiliation has always primarily been to the Avengers over the mutants, so it shouldn't be a surprise that she leans away from them.