Doubt

I think that the "I" in this song is turning the "you" from a thiest to an athiest.

There are really only two ways to know this for sure. First, the name of the song is doubt. Secondly, and more importantly, there is this verse:

i've come to plant the seed of gradual decay swallowing your faith entirely

The only time that the thing that's decaying is mentioned is here - and it's your faith.

This is supported by ideas like poisoning safety (religion is often a safety net), confidence dying (you were wrong about something as important as religion, so you feel like you know nothing now), the fact that you feel "it" burning (that is, the truth is taking root in you and you're trying to fight it, but you know it's right). Furthermore...

Self-sycophant Grotesque arrogance Bursting with shallow conceit

All 3 of those ideas above are often associated with those who are religious. Well, to be fair, they're really just associated with anyone who's really, really sure of their position. However, these three lines were said from the position of the "I" in this song.

Now, for whatever reason, this "I" is malicious. The "I" is clearly aggressively trying to destroy the other person's faith and is being really harsh about it (this should be obvious). I think that the opening paragraph is really good actually:

You'll know when this is done If you comprehend The calculated hate in subtlety

The "I" is extremely hateful because he's gone through meticulous calculation in order to do what he's done to the "you". It's like the difference between premeditated murder and spur-of-the-moment murder...premeditated murder is much more evil.

I'm not really sure what Blue Stahli's position on faith is. The athiest here seems to be correct in his views, but he seems to be malicious and hateful. Of course, for all we know, the religious person is a really bad person too. Stahli mentioned "self-syncophant", "grotesque arrogance", and "shallow conceit" earlier. It's hard to tell who is the good guy and who's the bad guy in this song. That difficulty could be a statement on the inherent badness of humanity regardless of who knows what is actually wrong or right...but then again, maybe I'm starting to dig too deeply.

Overall, in my opinion, this is a fantastic song with very well-written lyrics.

I agree and disagree with you. I agree it is an attack on religion, Atheism included, due to the fact people use it for their own selfish ambitions. I believe the writer is trying to show how hateful and personal people make the subject of faith. He goes to show that Atheists and Theists become hypocrites calling them "self-sycophant", "grotesque arrogance", and "shallow conceit". His voice in the song seems scornful and condescending. My personal opinion is it is about hypocrisy and defensiveness that people have when people place doubt in their own beliefs. I do agree with him trying to show that no matter what our beliefs the humanistic side of us will come out during conflict.

Its about someone changing a person,demoralising the person and has "deformed" the persons soul "I have come to plant a seed of gradual decay" Firist step of the "someone" that is changeing the person and meaning evil to the person.Then the second step is "i'm watching as it feeds on insecurity leaving you with nothing" Is when the victim has no control over that "someone".And the thirid step is "Pushing this through The weakness in you infecting you with this disease" when the powerful "someone" controlls the person completly.The last step is where that "someone" fades away and all its left is the consequences "Deep down inside you Too far to undo When all your confidence dies" Its the effect left behind. The song is whritten from the perspective of the evil "someone".The part when it says "You feel it burning Twisting and turning i hope this eats you alive" is the hate that the victim feels about that "someone" :D