When I was a young child, I used to watch this cartoon during the early 2000s, premiering on Nickelodeon. It was about kids who traveled through space with aliens that looked like penguins, in a blue retro futuristic looking spaceship. The entire series had a retro futuristic (60s style) science fiction aesthetic, surreal colorful planets and crazy gadgets. The art style of this cartoon series itself looked very similar to Jimmy Neutron, but it was definitely not Jimmy Neutron, although it was probably made by the same studio. It was called like "Space Penguins" or something. These penguin looking aliens had distinctive personalities, including an arrogant captain, a skinny nerdy scientist, and a fat awkward pilot.
Haven't ever seen this show myself but a quick Google search (cartoon + space penguins) returned a show called 3-2-1 Penguins that seems to fit your criteria.
It does indeed fear two human characters, a boy and girl travelling on a spaceship with penguins. Air date appears to be a match too as the Wikipedia entry states early 2000s.
You can see the full wikipedia entry here. https://en.wikipedia.org/wiki/3-2-1_Penguins!
Additionally there seem to be many episodes on Youtube for example...