Ghost Rider's supernatural powers and invulnerability give him tools Spider-Man cannot counter.
Spider-Man's agility and spider-sense make him incredibly difficult to hit, and his intelligence could help him identify Ghost Rider's limitations. But Spider-Man fundamentally lacks the tools to defeat a supernatural entity. His webs, punches, and kicks damage the physical host body but cannot affect the Spirit of Vengeance within.
Ghost Rider's hellfire is a mystical attack that burns the soul. Spider-Man's durability is impressive for a street-level hero, but he has no defense against supernatural flame. His spider-sense would alert him to the attacks, and his agility might let him dodge for a while, but Ghost Rider's chains can track targets and hellfire can be projected in wide areas.
The Penance Stare is less devastating against Spider-Man than against most opponents โ Peter generally fights to protect people, not to cause suffering. But he has still caused collateral damage and pain throughout his career, and the Stare would still be extremely painful.
Ghost Rider's hellfire burns the soul, bypassing Spider-Man's physical durability. The Spirit of Vengeance cannot be defeated by physical attacks, and mystical chains can track targets regardless of agility.
Spider-Man's spider-sense and agility let him dodge Ghost Rider's attacks, and his intelligence could help identify the entity's limitations. Peter's relatively clean conscience reduces the Penance Stare's effectiveness.
Ghost Rider wins through supernatural powers Spider-Man cannot counter. Peter can dodge and survive longer than most, but he lacks the mystical tools needed to defeat the Spirit of Vengeance.
Ghost Rider also fights
Spider-Man also fights