Pi's lifeboat = faith
Island = Religion
Sea and Sun = harsh realities of real life, scrutinizing your faith
Trees = clergy/priests/rabbis/imams, etc.
Meerkats = followers of religion
The overall message of the chapter is that although religion (organized faith) can aid us and stabilize us and nourish us spiritually in the short term, it is not a viable long-term answer to our spiritual questions, and will ultimately kill us mentally and spiritually.
Pi discovers the island when "I turned over to my other side," ie turning away from the practicality and the faith that had got him this far.
The survival manual tells Pi to look for green. And the island is green. "In fact, it was chlorophyll heaven. A green to outshine food colouring and flashing neon lights. A green to get drunk on." (and is religion not the opiate of the masses? Pi later refers to it again as "intoxicating") In other words, impossibly green. Too good to be true. Also, Pi tells us, "It is the colour of Islam. It is my favourite colour," directly associating it with religion, while also letting us know it is exactly what he wanted to see: "To take in green, after so much blue, was like music to my eyes."
Up until he reaches the island, Pi does not choose a specific religion he simply wants to "love God." When he is on the life boat, Pi treats all religions equally. "Vishnu preserve me, Allah protect me, Christ save me," he yells when his life is in danger. But on the island, he abandons Christianity and Hinduism, seeing only Islam: "As my heart exalted Allah, my mind began to take in information about Allah's works."
Unlike the turbulence of a lifeboat in the middle of an unpredictable ocean, the island was organized. It had "hundreds of evenly scattered, identically sized ponds with trees sparsely distributed in a uniform way between them, the whole arrangement giving the unmistakable impression of following a design."
But Pi's logical mind, which had served him so well on the life boat, allowing him to scrutinize his faith (and make it stronger), doesn't fare so well on the island. "It was then that I believed, and the only thing that sank was my mind; my thought process became disjointed." When presented with the miracle of live-giving fresh water ponds floating in the middle of a deadly, salt-water ocean, "I did not ask myself why the algae did this, or how, or where the salt went. My mind stopped asking such questions. I simply laughed and jumped into a pond." This is why Pi stays so long on the island. Under the watchful scrutiny of the sun, it seemed a literal garden of Eden, unaware of its deadly night-time nature.
Unlike true land, which has soil and mass, the island seemed unaffected by the ocean of real life, and "waves that fell upon the island simply vanished into its porosity." Pi is so sure of its ability to withstand the ocean that he "would have trusted staying on it during the worst hurricane. It was an awe-inspiring spectacle to sit in a tree and see giant waves charging the island, seemingly preparing to ride up the ridge and unleash bedlam and chaos-only to see each one melt away as if it had come upon quicksand. In this respect, the island was Gandhian: it resisted by not resisting. Every wave vanished into the island without a clash, with only a little frothing and foaming."
Unlike religion, faith (the life boat), on the other hand, is tossed about by the sea and bleached and cooked by the sun (the harsh realities of real life). In the lifeboat, Pi comes close to capsizing and drowning. Not so on the island of religion. In fact, the "island, coated with such tightly woven, rubbery vegetation, was an ideal place to relearn how to walk. I could fall any which way, it was impossible to hurt myself." Religion was just what Pi needed after the spiritual crisis when he had gone blind and lost his way in the previous chapter, and his animal savagery sacrificed another spiritual seeker who had lost his own way (the Frenchman, adrift in his own boat, devoured by Richard Parker.) It was this crisis, in fact, which had lead to Pi's tearful repenting and regaining of his sight which allowed him to find the island in the first place.
But even on the island, Pi was still afloat at sea. The island was free-floating, not attached to real land, which was Pi's ultimate (spiritual) goal, so it did him no real good.
The meerkats, of course, are the followers of religion. They have given up rational thought, allowing Richard Parker to kill them, "devouring one meerkat after another, blood dripping from his mouth, and they, cheek to jowl with a tiger, were jumping up and down on the spot, as if crying, 'My turn! My turn! My turn!'" They had accepted the religion entirely.
To Pi, their lives are empty and boring, consisting only of "pond staring and algae nibbling" from which "nothing distracted the meerkats," even death itself. Indeed, Pi found the island itself empty and boring, "unvarying in its features. The same blinding greenness throughout, the same ridge, the same incline from ridge to water, the same break in the monotony: a scraggly tree here and there."
The trees are clergy/priests. Their "roots did not go their own independent way into the algae, but rather joined it, became it. Which meant that these trees either lived in a symbiotic relationship with the algae, in a giving-and-taking that was to their mutual advantage, or, simpler still, were an integral part of the algae." Pi seems fairly sure that the latter is the case since he doubts "that an independent organism, however intimate the symbiosis it has entered upon, would give up on so essential a part of life as reproduction," just as clergy frequently take on a life of celibacy.
When you think of religion, you think of the clergy. They are the visible part of a religion, attracting people with their charisma. Similarly, it is the trees, attracting Pi to the island "The trees were beautiful. They were like none I had ever seen before. They had a pale bark, and equally distributed branches that carried an amazing profusion of leaves. These leaves were brilliantly green, a green so bright and emerald that, next to it, vegetation during the monsoons was drab olive."
Also, it is the trees that the meerkats cling to when danger comes, not to the island itself. Pi, too, is taken by a particular priest, "I sang that tree's glory, its solid, unhurried purity, its slow beauty. Oh, that I could be like it, rooted to the ground but with my every hand raised up to God in praise! I wept."
The carnivorous tree with the teeth-fruit represents the highest order of clergy, the "pope" of the island. Pi refers to it as "the forest equivalent of a queen bee." He finds the pope-tree at the center of a densely populated grove of very tall trees, ie, high-ranking clergy, where "the sky was quite blocked off, or, another way of putting it, the sky was solidly green." Religion comprised the entirety of existence in this location, blocking out the realities of the sun, sky, and ocean. The promising, orange-sized fruit offered by this tree proved to be nothing but a single tooth wrapped in leaves--the spiritual death masquerading as fruit, disguised by the promises of religion.
So although the island saved Pi's life, nourished him and restored him to health, protected him from the ocean and the sun, provided him food with no effort on Pi's part, gave him meerkats to keep him company, he consciously chose to leave because he "preferred to set off and perish in search of my own kind than to live a lonely half-life of physical comfort and spiritual death on this murderous island." And though he tries to take some of the algae away with him when he leaves on the lifeboat, he discovers it cannot exist independent of the island itself.