Thing with Marvel is that if he doesnt beat Thor fast, hes bound to run out of magic energy. Plus you have to take into fact that Enchantress was amping him that whole fight. Maybe except for the last few blows, but Cap still had the advantage for a bit.
RKT can tap infinite amounts of energy. Cosmic, Magical, Elemental, Etc... Yeah, Thor curbstomps him. With the Runes, he has all knowing knowledge... And knows how to use that power.