There aren't too many Marvel characters who can beat Batman - or characters anywhere, for that matter - but there are a few who would give the Dark Knight a run for his money. Look, Batman is a lot of people's favorite character, but at the end of the day, he's just a guy in a bat costume. Bruce Wayne is not exactly Superman (and even the big, blue boy scout has some Marvel characters who could take him out).
Batman's best tool in his favor is his plot armor. He's the hero of his story, so he has to eventually defeat the villains he takes on. However, there are a lot of Marvel villains that either have a unique advantage against Batman, or are frankly just too highly powered for a mortal like him to stand up against.
Molecule Man Is Powerful Enough To Destroy Galactus With A Single Thought, So He Could Certainly Do The Same For Batman
Owen Reece, AKA Molecule Man, has the ability to control the molecular structure of virtually anything. Although he began his life as a normal man, one nuclear mishap later and many now consider him to be the most powerful being in the Marvel Universe. Eventually, the Fantastic Four even discover that his demise would trigger the end of the entire universe.
Molecule Man's powers are so immense that Doctor Doom once channeled them and restructured the entire universe. After this event, Molecule Man is treated with a lot more respect in the Marvel Universe. In one story, upon entering his presence, Galactus remarks that Molecule Man can destroy him with a single thought.
In his original incarnation, Molecule Man may have toyed with Batman by turning his Batmobile into a rubber ducky while he is driving. However, in more modern stories, Molecule Man most likely would just alter reality so that Gotham itself, and thus Batman, never existed.Tough match for Batman?
Pitting a world-devouring galactic entity like Galactus against Batman may seem cruel, but he's a good representation of the scale of villain that heroes have to face in the Marvel Universe. Galactus is so powerful, when he shows up to devour a world, there's virtually nothing any civilization can do to stop him. The Fantastic Four only defeat Galactus when he comes to Earth because the Watcher leads them to a weapon known as the Ultimate Nullifier in Galactus's own armory.
Galactus also has the ability to imbue whomever he wants to with the Power Cosmic. Imagine if Galactus chose to grant a certain someone's rogue's gallery with the Power Cosmic. Galactus wouldn't even have to lift a finger if he made Joker and the Riddler his heralds.Tough match for Batman?
Batman is brilliant, but he is really no match for the brains of Doctor Doom and Mr. Fantastic. Batman is a master strategist, but Doom and Reed create world-changing inventions on the daily. They aren't fashioning grappling hooks; they're constructing inter-dimensional portals. Batman can never clean up Gotham, but Doom can certainly make Latveria one of the safest places to live for his citizens (as long as they obey the supreme will of Doom, of course). Then, after Doom has cleaned up Latveria and while Batman is still working on Gotham, Doom can go after Batman with the entire might of the Latverian army.
Even without being the sovereign ruler of a country, Doom is an incredibly powerful sorcerer. Doom is next in line to be Sorcerer Supreme, once losing the trials to become the new Sorcerer Supreme only to Doctor Strange himself. During Secret Wars, Doom became the most powerful being in the universe and constructed everything that exists in his own image for his own purposes. Doom is not to be trifled with, not even by Batman.Tough match for Batman?
Batman typically deals with villains attempting to take over the city of Gotham. In contrast, Annihilus operates on a much larger scale, laying siege to entire planets and even universes.
Annihilus commands the Annihilation Wave, which is a fleet of ships and bugs so powerful, they've decimated galaxies. This fleet consists of over 15,000 warships. And, as a reminder, Batman's fleet consists of a few Bat-themed vehicles. During the Annihilation event, Annihilus slaughtered over a million worlds. The battle with Batman would be over before Annihilus even knew it began.Tough match for Batman?