My Gym Partner's a Monkey/WMG

It's all a massive coma hallucination on the part of the main character.
On his way to school, Adam Lyon was hit by a car and became comatose. He then proceeded to hallucinate that he went to a school full of animals, because what young child wouldn't love that?
 * Adam, given some of his horrible times.

The school is a secret, black-ops genetic research facility.
The school only lets "animals" in to hide the human/animal genetic hybridization that they're doing to create a race of intelligent animals to use as living weaponry. Adam is inserted into the school to spy on the horrific results and report back to unseen superiors.
 * Alternatively, Adam is there to provide the raw human genetic material for the hybrids.

The series is thinly-veiled racist propaganda.
The theme song talks about how the main character, Adam Lyon, is sent to an animal school because "L[i]on's my last name", which sounds suspiciously like anti-Semitism. Besides that, the show obviously reflects "Jim Crow"-style racism against blacks: animals are only allowed to go to special, "animal" schools, and they are shown as uncontrollable savages on many occasions.
 * This goes with my theory that Jake is a black kid and Adam is a HUGE racist.
 * Take into the consideration that you all are racist for even thinking that.
 * He made a show about a kid going to a school full of animals and that's it. What, is everyone supposed to avoid making anything in which anyone is outcast or they'll be called racist? Only an idiot would really think a cartoon that has animals that go to their own schools is racist. And while I'm at it, what has Adam ever done to make himself seem like a HUGE racist?

Jake harbors a strong homosexual lust for Adam.
Seriously here, pick any episode and you can find at least three blatant hints of this.

Adam is a Lion
Not only is he a lion, but he is also the toughest and most dangerous creature in the school. But he has multiple personalities, one of which is Adam L"y"on.

This is why Principal Pixiefrog is so quick to blame Adam for everything and why Adam survives all those Amusing Injuries. Anyone who strays from Adam's delusions is harshly punished. Ingrid's and Jake's attractions to him are because of their natural attraction to an alpha-male: the L"y"on personality isn't one, but the L"i"on personality is.
 * That puts a really chilling spin on Adam's parents.

Adam is insane and believes a normal school is an animal school
His human friends show up once in a while when the madness wears off. Sometimes it doesn't wear off right away; that's why his female love interest shows up in a giraffe costume. This explains the costume; if the world of the show is what it appears to be, then wearing that costume would be like wearing blackface.

Adam is the only human left on earth.
The others tolerate his imaginings of his human friends out of pity.

Adam has a weird imagination
He probably mistook an academy for geniuses (or a private school, as that shark isn't really smart) for an animal school, and is imagining everything. The other "animals" are kids who mostly reject him because he has issues; since Jake also has psychiatric problems and is a furry, he likes Adam's imagination.

Everyone's human. Jake's just been feeding Adam hallucinogenics since they met.
Because Jake's enough of a Jerkass to enjoy it.