I think That this song Refers to 'the faithful' (Abrahamic religions) jealously and desperately clinging on to religious principals.

"Wear the grudge like a crown
Of negativity
Calculate what you will
Will not tolerate
Desperate to control
All and everything
Unable to forgive
Your scarlet letterman"

--Describing the self assumed rightousness and self interest of "the faithful". Then mentioning being "unable fo forgive your scarlet letterman", presumably refering to the First Council of Nicaea or the Book of Common Prayer and therefore the bearers of Christianity.

"Clutch it like a cornerstone
Otherwise it all comes down
Justify denials and
Grip 'em to the lonesome end

Clutch it like a cornerstone
Otherwise it all comes down
Terrified of being wrong
Ultimatum prison cell"

--Decribing clinging on to the organised religion for fear of loss of rightousness and self-denial of wrongdoing.

"Saturn ascends
Choose one or ten
Hang on or be
Humbled again
Humbled again"

--Saturn, in astrology, is associated with (among others) limitation, restriction and structures. The rise in negative emotion is also suggested.
This probably refers to the percieved collapse/ing of traditional religious beliefs and structures. Choosing one or ten, could be preposing that "the faithful" either cling on to orthodoxy and continue or accede to new ideas but be humbled for thier earlier ways. This is because saturn was traditionally considered the ruler of the first house but is considered ruler of the tenth house in modern astrology.

The rest of the song pretty much repeats the theme with slight variation until the end.

Towards the end, the lyrics extol allowing the religious beliefs to die and therefore allowing the rebirth and enlightenment to occur.
The return of saturn also signifying a turning point in someones life.

I think that the organised church (or the hierachy) could be the target or it could be the individual believer. Holding on to religion for fear of having to let it go and of being unknowing again. Knowing tool it seems likely to either, although in retrospect it seems more likely to be the individual since the theme of Lateralus is individual enlightenment and self-realisation.

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