We get several conflicting messages about what exactly is the religion of LOST. First, the primal principle seems to be to protect the Light in the tunnel. Everything that happens on the island ultimately revolves around this one crucial point. It's the smoke monster's mission to destroy the light so he can get off the island and it's Jacob's mission to protect the light so that...what? So that evil won't take over the earth? Or that the underworld won't take over the earth? Its not fully clear.
We also have to change our definition of good and evil to make them more relative. Presumably Jacob approved of the mass gassing (aided by the young Ben) of the Dharma Initiative. The Dharma Initative's quest to unlock the scientific mysteries of the Island came into direct conflict with making sure the Island stays protected and the light, or darkness, doesn't escape. Other crimes by Jacob and/or the Others and/or Jacob's mother (his predecessor as protect of the light) include: bashing in the head of pregnant mother, stealing children, hanging Charlie, kidnapping Claire and experimenting on her, killing Juliet's ex husband in the real world, kidnapping Walt while shooting at his father, Jin, and Sawyer and leaving them for dead, killing Naomi (who was killed by Locke, presumably getting his psychic cues from Jacob or the island), etc. None of these things seem like they fall under the category of "good" but lets not forget that in a war all things are relative.
Arjuna, for instance, in the Bhavagad Gita, is lectured by Krishna that he must fulfill his Dharma, i.e. take up his sword and potentially kills his cousins and uncles if need be in order to protect his family, kingdom, and army. Thats his dharma. And Moses, of course, in order to free the Hebrew slaves, must release untold punishments on not only the Pharoah and soldiers of Pharaoh, but on ultimately the most innocent of babies within the kingdom of Egypt. Nobody disputes that Arjuna or Moses were on the respective sides of their God. And this can be concluded for Jacob as well.
But something more appeals to us about Jacob and about the religion of Lost: the idea that it is a religion of the lonely and broken.
Sawyer complains that his life has gone from bad to worse ever since Jacob first brought him to the island but Jacob reminds him that he was already lonely and broken as were all of the other candidates. Its somehow fulfilling and special to know that when hope is lost, when you are either imprisoned physically (as Kate and Locke were) or mentally (as Sawyer and Jack were) or by just a run of bad luck (as Hurley was) or imprisoned by family/husband/wife (the Kwons) that out of that imprisonment something happens that can free you and make you special. A candidate. But do you have to be chosen by Jacob to be a candidate? Not necessarily. Jacob crosses Kate off the list for almost arbitrary reasons. She had become a mother and devoting yourself to child is as important as devoting yourself to a god. But, he says, "the job is yours if you want it." So it is for all the lonely and broken. We can step up and become a candidate, have a mission in life to protect the Light that is hidden from most. Protect it and serve it and, in the end, having faith in that purpose seems to bring serenity and purpose, if not wisdom.
The most appealing scene to me was when Jack and Sawyer were on the boat escaping from MIB when Jack decides to jump off the boat because "the island isn't done with me yet". Jack took six seasons to fight the demons that were clouding his inner voice, the voice that spoke in unison with the island (which in itself was a representative of God). Those demons included his drug abuse, his belief in science, his fear of his dad, his insecurity about Kate, his insecurity about his skills as a medical doctor or his skills as a leader. Once he realized that there was a higher purpose, and that purpose had no other mission than to listen to that inner voice, then all of those little demons that were battling him, quickly disappeared. The fight was over. Not only was it fate that guided him but an ability to truly tie into the voice of the Universe/Island/Jacob/Light and act on its wishes. By leaving the boat at that moment, he had no idea if he was doing right or wrong. He just knew he had to do it. He was meant to do it. And by surrendering to a higher power - a power you can't even understand but fully giving yourself to it as its servant - inner peace results, salvation is a possibility, and things in the world start to coalesce around you so that you feel a higher purpose or power is taking care of you and moving through you.
Fighting that impulse, as he did for the first five seasons, only led to the anguish from season four when he was begging Kate, "We have to go back!" despite his having achieved every goal he had ever wished for (escape from the island, marriage with Kate, freedom from his Dad, success as a doctor). The only success that's ever important is peace with yourself and being in tune with that inner voice so that both your voice and the inner one speak the same.
And then, like all good religions, this is not just philosophy but magic. Moses parts the red sea. Jesus turns water to wine and raises the dead. Krishna can change shapes and raise armies with the snap of his finger, etc. By succumbing to the wishes of the island, all good things can happen. You can win a lottery, you can walk again, or get cured from cancer, or ward off both the outer and inner demons that formerly would plague you. Things happen, and gratitude is the best way to acknowledge it, as Locke continues to do until his death.
So what to make of it? Tuning into nature, spending time listening and acting on that inner voice, protecting the light thats inside of you so the smoke monster can't extinguish it, listening to the subtle nudges that the Universe gives you and acting upon those nudges. All of these can turn you from a simple viewer of a drama to potentially something much greater. A candidate.