Ok ok ok. Now, I say that Lost did finish on the faith side, a bit... but let's get a few things ordered. When I see people saying it's just like Jesus, he just IS GOD. Um hold on a minut. Lost got spiritual, but it did not say "have faith just because"... quite the opposite. JACOB WAS FLAWED, he brought harm to his brother, he ignored the crime committed on his mother and he exploited people weaknesses, manipulating them through their lives to bring them to the island regardless of their will. We know that those were just Jacob's rules, and Hurley seems to have been able to run the show the Hurley way (can't wait to see that!)
The story on the character line to me is not, "answers don't matter"... lost gave tons of answers which is why we expected some of the big outstanding ones... but not getting them doesn't mean they don't matter, just because answers create more questions. The real issue about faith is that blind faith is not a good thing... it might work out... but it doesn't pay off quite as expected (you don't transport home, e.g.). The point with Desmond and Charlie was that Desmond was willing to let Charlie die to see Penny. The issue wasn't about "could he change that" it was the character struggle, "would he want to change that"... and Desmond's character paid off in that he couldn't help but at the last moment want to help Charlie, or at least warn him and let him take control of his own destiny.
This is playing with the ends justify the means... and Lost handled it well, it's an area to be ambiguous about. But they definitely showed that doing things by faith is not a good thing... it leads to resentment, it leads to ruined lives, and I suspect Hurley won't be doing the same murder and manipulation games that Jacob imposed with his version of the rules.
They all went to a spiritual place that was based on relationship, growth, sharing time... not on the god head. They "created" that place "themselves"... it was not a god-head that created that world, not a "Jacob", just them. Yeah, very spiritual, but check your spirituality to see how compatible that view is with Lost. Jacob manipulated the whole situation, knew where it was going, Ben had little choice, or rather, was manipulated out of that choice by a system of secret rules and lies. Jacob created "the good" as people that killed at the drop of the hat, from Dogen to you name it... and if this was just so Jacob could pretend not to be responsibile, that's sickest of all. A rule system that says planting a bomb which won't go off unless you try to disarm it, can go off if someone disarms it... is messed up. We have to think those are Jacob's rules, that Jacob like his mother has the power to grant immunity from time and fatality and that's how he used it.
And don't get me wrong, I love this. I was VERY worried that Jacob might turn out good, and the show might say, "the ends justify the means... the good god-like guy says, kidnap, you do it... faith is rewarded, if you have to massacre, just do it, as long as it's for the good."... but it totally DID NOT say that. Instead, the MiB became a monster sure... but I think the murdered-mother, raised-by-a-kidnapper, killed-by-your-brother-or-near-as, thing explains how he became the cages monster in Jacob's maze of horror.
All the condescending sanctimony in Jacob's manner turned out to be intentional... he is no different from all the other's that claim to be the "good guys"... as Frank said, "that means they're the bad guys". So while it's spiritual, that doesn't make it religious or into organized hierarchical shut-up and don't ask questions system like Jacob liked. That is, it was against fanatacism, imo, but not again spirituality. And in the end let me say it is certain that Lost is PRO-ANSWER. People seek answers and find them, the most important being about themselves, and what their problem is... but people do seek answers, and those that hide answers were always manipulating and lying. So Lost is pro-answer, pro-spiritual, and did not say that faith is rewarded. Many people had faith it got them nowhere in life, not until, in death, John let go of his faith did he move on. In life his faith was entirely used against him, almost successfully.