The Minecraft Theory-
In the beginning, people thrived. Cities of wood rose, strongholds of stone took hold. For millennia kingdoms existed. All was at peace.
Then came the nether.
At the edge of the known world, a large fissure formed. It lead infinitely down into a living hell. From it came spiders, skeletons, creepers, and the disease that spawned zombies. These demons were able to withstand the moon light, but only the creepers and spiders would not be burned during the day(the sun warms the hearts of spiders though). Eventually the hole was found and there was much conflict on what to do with it. An expiditionary force was sent down to explore, and what it discovered the mineral known as nether rack. It was brought to the the surface for research, as well as being compressed into netherbrick to build fortresses inside the nether. But something happened to the people down there, the zombie virus was much stronger in the nether and caused them to mutate into abominations that were still somewhat intelligent(zombie pigmen).
Back on the surface, all hell had broken loose. Governments were collapsing, kingdoms constantly at war with each other. In fact the conflict was so violent that a large battle caused the destruction of the fissure that lead to the nether. All of this was a result of the nether rack that had been brought up. Exposure to the mineral caused anger, spite, and bloodlust. Soon everything fell apart, and those who had resisted the effects sought a way to fix such a massive mistake of humanity.
They sought refuge in a place that had only existed in myths and legends.
They sought an end.
Thus, an inter-dimensional portal was created to seek another world, one that was untainted. One was found, but it was a dark and desolate land, and its sole inhabitant was a massive dragon of unkown origin. A majority of the last humans through anyway, but the "end" realm, as it was called, was different. It changed people, turned them into exact copies of each other. They became endermen.
The portal was destroyed after endermen began coming through and wreaking havoc, but some still remain. How they breed is unknown, as well as how they obtained their "abilities".
Now there was only a few hundred humans left in the world, surviving in small villages. Eventually we re-evolved into the peacefull NPC villagers.
Centuries passed, and things finally came to a relative calm.
Then, Steve appeared.
Deep underground a machine had been built at the time of chaos, a machine that was meant to bring salvation to humanity once the apocalypse was over. This machine was meant to breed a man, a man that was immortal and had inherited all human history and recorded knowledge. Not only that, but he was genetically altered to be immune to the zombie virus as well as the effects of the netherrack and end realm. It teleported Steve to the surface and self-destructed, for it was of no more use. Steve was programmed for three things- survive, repopulate, and kill the enderdragon, for it threatened to reopen the portal between the end and the earth. Other spawning devices are scattered across the land, but they are set for a later date.

That is why everything is as it is.
Still a bit choppy but you get the idea.

Other explanations

Iron/Snow golems- They were once sentries used in the wars of the great conflict. Steve inherited the knowledge to create one.

Nether Portal- A failed design for an ender portal. Steve inherited the knowledge to make one in hopes of destroying it.

Herobrine- He is the spirit of humanity. He is not evil, but is merely watching over Steve. This also explains respawn.