Because Im a halo fanboy I must somehow refute this...
I KNOW The Master Chief knows how to operate the weapon system of any capital ship. I dont care who you are a nuke/mac round/fifty millimeter chain gun hurts
Me, I am also a Halo Fanboy. (wH00T!! ARGUMENT!!!!) I bet a MAC round could damage a Space Marine Ship, but look at the name: "Space Marine". A few of them could fly over in a Thunderhawk(heavily armored Dropship/transport) and drop a few squads of Space Marines inside the ship. Then you would be screwed because Master Chief's weapons and the Covenant weapons wouldn't do shit to Space Marine armor. except scorch it and possibly scratch and dent it a little.
Space Marines in Terminator Armor are walking tanks. Equipped with missiles, storm bolters(gattling guns) Plasma guns(flamethrower-like weapons that spew out an extremely hot, plasma liquid that burns through anything), Chainswords(swords with chainsaws for blades) and power fist(hydraulicly-powered armored fist that can punch through almost anything).
Nothing Master Chief has could take down Terminators. A Space Marine may go down if his head is hit with a rocket or something like that, but these guys move so fast, it'd be pretty hard to hit one with a rocket. They have accelerated bodily functions(if hurt they can heal extremely fast in a few seconds).
The Librarian Space Marines are like Jedi, except they only shoot lightning. They wield staffs with blades on the end and they surround the staffs with their lightning. One of these guys could overload Master Chief's suit, leaving him immobile in his heavy armor and essentially human. The other Marines could then fire off their weapons and reduce Master Chief to bloody chunks of fried meat and metal.
Space Marine ships have craploads of laser batteries(turrets) and they're huge. (bigger than any ship Master Chief could get.)
Picture like 30 Pillar of Autumns stacked together. 10 long and 3 high. Space Marine ships have a couple hangars and launching decks. That;s a lot of ships, more than enough to mop up Master Chief's fighters.
Master Chief couldn't even take down some of the species of Aliens the Space Marines fight. The Eldar are a highly advanced race(more advanced than Space Marines). They have psykers that could make Chief's head explode before he even draws his pistol.
Plus, there's thousands of Space Marines in battles. They don't fight for a continent. They fight for entire planets. They'll sweep from one side of the planet to the other, eradicating all that stand in their way. They would carve through Chief and his Marines, like a chainsaw through butter.
So deal with the fact that Master Chief wouldn't stand a chance against a Space Marine.