Planet 51/WMG

Chuck Baker is a distant ancestor of Zapp Brannigan from Futurama.
Because it makes me laugh. Really, that's all I've got.
 * Makes sense. Chuck is supposed to be a likable, but he's really just a more tolerable version of Zapp.

The government in Planet 51 is suppressing ALL alien contact, because it's at a galactic crossroads.
There's more than one dome where the rover was being kept. The "official story" from the government is that the universe is 500 miles across. Somebody is suppressing something....
 * 500 miles across? What is this, The Truman Show meets Men in Black? Oh wait, I get it: The Village.

"51" in the title refers to AD 1951, the Earth year corresponding to the tech and cultural level of the society near where Chuck's craft landed, not necessarily Area 51.
Chuck mentioned someone coming back once the culture hit the sixties.
 * Interesting, but that would imply that at the turn of 1949-1950 all of a sudden girls were wearing poodle skirts and cars spontaneously sprouted tail fins.

The reason General Grawl is so forgiving in the end is because he has planted the alien dog on Captain Baker's spaceship to ensure that the human never returns to earth.
Think about it - the alien dog pees acid. Can you say "hull breach"? I knew you could.
 * Forget hull breach, the dog is an expy of an Xenomorph, and you do know how they reproduce.
 * Maybe Captain Baker is the Space Jockey!

Planet 51 is fifty-one lightyears from Earth.
Assuming humans in the movie could actually get there at the turn of the 21st century, it could account for the similarity in culture, language, and music if Aliens Steal Cable in the form of radio and TV transmissions (though obviously the TV would be audio-only). It's quite a stretch, but considering the improbability of everything in the film it's entirely possible.

Chuck Baker is not an astronaut at all.
Think about it. Does he seem like a highly trained astronaut? Throughout the course of the movie, we learn that he doesn't "have the right stuff", he isn't brave, he doesn't know how to drive his own ship, and he's just about the stupidest, least capable man you could ever find. It took like five minutes to finally realize that he wasn't walking on a barren planet. There is no way NASA would ever trust a man like that on an actual space mission. Chuck Baker is actually the most annoying and obnoxious person on Earth, and everybody just got tired of having to deal with him. So they fed him a story about going on a very important space mission, gave him a space suit, then shot him to the furthest reaches of the universe they could find.
 * To be fair if you landed on a planet populated by brain sucking aliens without a single weapon even the most hardened 'naught would hide.
 * So you're implying NASA spent billions building a self guided rocket just to get rid of one idiot? Even the government isn't that extravagant...they would at least use 5 idiots.
 * Why, of course, the other four idiots are on the ship orbiting the planet.

It Was All Chuck Baker's Dream
Chuck Baker is being sent on a ship to find intelligent life, on a planet at least 51 light-years away. It has to take a long time to actually actually accomplish this. So, Chuck Baker is in a stasis box/hypersleep/a block of carbonite, and dreams of accomplishing his mission, and even finding a planet almost exactly like Earth.

Chuck is gay
That's the reason for all the Ho Yay. He does mention getting a lot of women, but that could be an act because the planet is so much like Earth, that being openly gay there would be like being openly gay in 1950's America. Also, it's a kids movie.

The residents of Planet 51 count in a different base
Human beings use the decimal/denary system. That is, we count in sets of 10, most likely because we have 10 fingers. (e.g. the numbers 1-10, 11-20, and so on.)

The aliens have 4 fingers on each hand; therefore, presuming they start counting at 1 and understand the concept of zero, they would have the numbers 1-8 before looping back around to 109, 119, etc.. This numeral system is called nonary, or... Base 9.

Alternatively, they have 8 digits (0-7), and the pun doesn't work any more.

Planet 51 was a colony planet.
Back in the distant galactic past, Planet 51's inhabitants were a mighty empire, spanning hundreds of worlds. Something happened to break up that empire, cutting the Planet off. Their society descended into chaos, and "rebooted" in the form of a stark 1950s-esque culture. To prevent another societal catastrophe, Base 9 was founded...which soon discovered its dark past. What followed was an extensive attempt to hide any clue to the true nature of space, and thus stop people from discovering the grim truth.

With all of that said, you'd think the inhabitants would stop and think why their world is named "Planet 51" (and, in the original script, "Planet 1").