Their actually does seem to be a FAQ site that addresses some of the questions about the monster. I thought they did a good job.
Possible spoilers, read thread at your own peril.
Where does the monster come from?
The producer J.J. Abrams says, "The concept for the monster is simple. He's a baby. He's brand-new. He's confused, disoriented and irritable. And he's been down there in the water for thousands and thousands of years."
And where is he from? "We don't say deliberately," notes the writer, Drew Goddard. "Our movie doesn't have the scientist in the white lab coat who shows up and explains things like that. We don't have that scene."
The film does give us clues. You can clearly see an object flying into the ocean behind Rob and Beth in the closing shot, though Abrams has stated that this is a satellite, which was part of the marketing campaign for the film.
Note that in the "viral" marketing campaign for the film, there were hints concerning the "Bloop" incident. In 1997, the U.S. National Oceanic and Atmospheric Administration recorded an ultra-low frequency underwater sound that was never identified. Scientists who studied the phenomenon said that the creature that produced it would be much larger than a blue whale.
Also in the viral campaign were several news reports concerning the destruction of an oil drilling rig, further linking the creature to the deep ocean.
What could account for the monster's size and power?
There is a phenomenon known as deep-sea gigantism. The term means that some creatures, who are relatively small when conceived near to the surface, get progressively larger as they develop deeper and deeper in the ocean. For example, squid are usually a maximum of 60 cm in length, but the Giant Squid, which can reside at depths of over 900 m, can reach up to 13 m in length. As for what kind of creature grew to that size, the monster does somewhat resemble animals in the amphipod order.
It could be posited that the monster was disturbed by the oil drilling rig and then followed a tanker ship to the New York harbor (the first thing it destroyed was a tanker ship), where it then proceeded to rip apart the city, finding it a threat. The little creatures that attached themselves to it could be ectoparasites that live on the monster.
As for the monster's seeming indestructible nature: living at depths near the bottom of the deepest parts of the ocean would mean the creature had to live under spectacular pressure, thus making its hide tough enough to withstand heavy rounds of artillery. This would also explain how it could survive so well on land for extended periods. In order to move around properly under the conditions of immense pressure in the deep ocean, it would have had to develop a powerful musculature; and while it is unlikely that it could breathe the air, the deep ocean is a low-oxygen zone, meaning the monster would have had to develop ways to absorb and process what oxygen it had available, as well as store it for long stretches of time.
If you follow the faux sites such as 1-18-08.com they describe a secret ingredient for a drink named Slusho. This ingredient named Seabed Nectar is found deep underwater under awesome pressure and in freezing temperatures. It is possible that this chemical mutated a deep sea animal and created the monster, or that the chemical came from the monster itself.
http://www.imdb.com/title/tt1060277/faq#.2.1.34