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In the recent movie Man of Steel, we can see Kal-El being weakened down by Kryptonian atmosphere.. there isn't any question about a red sun or Kryptonite.. he got weakened by the air breathing on his planet artificially created by the ship life support system.
I loved this movie but that specific point as been bothering me ever since !
How can the Man of Steel become so weakened by Kryptonian air when 20 minutes later he simply breaks the panel and breath easily in the vacuum of space ?
The Man Of Steel Answer Insight Commentary (MOSAIC) Podcast Episode 6 covers this topic fairly thoroughly.
However, let me give you the answer then you can listen to see the work / proofs / logic.
MOS Kryptonian super powers are powered entirely by Earth's Yellow Sun (this includes sensory abilities). That is the only mandate on having their powers. Thus their powers can persist in a vacuum, underwater, in an oil rig fire (which isn't normal Earth atmosphere), or in all the environments in between Earth and space.
Jor-El describes this using the metaphor of "drinking" and like water, you aren't only hydrated while you are drinking the water. You can also store the drink in your body to keep you hydrated while not drinking. This means Superman can exhibit powers even when not in direct sunlight.
However, a more apt metaphor is of a laptop with a removable battery and a power plug. The laptop will run on either battery, or plug, or both... but not neither.
The Kryptonian Atmosphere acts to unplug (but not drain!) the battery. Additionally, space ships are shielded against radiation. Therefore, being exposed to Kryptonian Atmosphere disconnected his battery and being on the Black Zero unplugged his power cord. So Superman lost his strength. After the Kryptonian Atmosphere was replaced (either by Earth Atmospherics OR vacuum), Superman's battery was reconnected and thus his strength immediately returned. He was NOT empowered by Earth's Atmosphere (otherwise vacuum would have weakened him). As for what Zod and company were breathing on Earth, we can't be certain, but even if they were breathing Kryptonian Atmosphere, they would still have power in the form of direct sunlight or a power cord (irrespective of a disconnected battery).
This theory is fully consistent with the entire film and the Podcast reconciles every instance (including the helmets and sensory "weakness"; and Superman briefly losing flight while fighting the World Engine) except the Prequel comic, but also explains why that example can be excluded.
As for why, mechanically, Kryptonian Atmosphere weakens Superman, it's a combination of two general factors: 1) He has organs and they work; 2) It's a biochemical reaction.
We know Superman tends to follow biological rules for a number of reasons, not the least of all is how Zod is stopped. Additionally, there's a strong suggestion that even with all his powers, Clark still biochemically reacts with the world... he drinks beer while watching football, implying that it is reacting with his body so that he can taste it. It is unlikely that Kryptonian Atmosphere is radiological simply because of how much was spewed into the air and Lois's exposure to it.
Therefore, it is possible that in breathing in the Kryptonian atmosphere, it reacts biochemically with his lungs and some other organ or process which allows him to metabolize stored sunlight energy, and therefore he becomes cut-off from his stores of energy. Just as sour may cause you to pucker, bitter to gag, spicy to pant, Superman's reaction to "tasting" Kryptonian air was temporary weakness.
Under this theory, if Superman had held his breath the entire time he was on the Black Zero, he would have been fine... but he also wouldn't have been able to speak and he would have had no reason to think to do so. Additionally, it's likely he would have eventually adapted. He did, nominally, in the sense that he didn't remain passed out and coughing, but merely powerless.
These are gone into more depth in Episode 7.
Via YouTube: Man of Steel Myths: How the Atmospheric Weakness Works
Man of Steel added a new source of Superman's powers (which to my knowledge hasn't been used in previous canons) in that he gains some of his powers from Earth's atmosphere. Specifically, there's something more nourishing about Earth's atmosphere than Krypton's. Early in life Clark adapted to Earth's atmosphere, this was the flashback where he was in a closet at school. When exposed to the Krypton atmosphere aboard the ship, it sickened him and disoriented him, as he had never been exposed to a non-Earth atmosphere before.
On the ship, Jor-El (the computer program) alters the ship's atmosphere to make it Earth-like, this then restores Superman's powers. Once he then flees the ship, we see that apparently a lack of atmosphere isn't harmful to him nor does it drain his powers.
See also this answer.
It has to be Kryptonite particles in the air. Kryptonite was all over his home planet. Superman never grew up in it like Zod and his race did. They need it to keep their bodies in check (Zod, etc). Breathing the "good" air of Earth puts them out of balance. Fine particles caused him to spit up blood and become weak.
I remember that the atmosphere of planet krypton has red sun radiation, all kryptonians run out of powers in these atfmosphere because the red sun is old. With the yellow sun of the earth , the cells of the kryptonian body charge regain strenght and the rest of powers. In these part is not kryptonite that damage superman in the zod ship. The atmosphere of Krypton has red sun radiation, in these conditions and witouth any type of protection , superman collapse, he feeling the radition for the red sun by first time, and loses his powers . The another are not afected by his armours. Since he takes the energy of the yellow sun , he reagins his powers.
In the film's official novelisation, it's made abundantly clear that spending time in an Kryptonian atmosphere weakens Superman. No special explanation is given why
“His body is rejecting our ship’s atmospherics.” Zod gazed down at Superman, who felt sicker than he had ever felt before. “You spent a lifetime adapting to Earth’s ecology, Kal. But you never adapted to ours.”
Superman struggled to overcome this unexpected weakness. His head throbbed painfully. His limbs felt like rubber. His vision blurred. Sudden chills alternated with feverish hot flashes, while pressure built within his ears. He heard Lois calling out from what sounded like miles away.
When it's time to leave the ship, he breathes in the "Earth-like air" and lo, his strength is renewed:
“It’s called a backup plan. Your ship’s atmospherics just switched back to Earth levels, which means I’ve got my strength again.” Steely blue eyes, with a hint of solar red, fixed on Jax-Ur. “So if I were you, I’d start running.”
Superman tested his shackles again. Straining beyond his limits, he ripped one loose, freeing his right arm. Jax-Ur’s sunken eyes grew wide. Coughing painfully, he staggered out of the lab as quickly as he could manage. He clutched the stolen blood sample to his chest.
Superman let him go. He took a deep breath, pulling the Earth-like air into his lungs. He felt his strength rushing back.
