And on [Redcrosse's] brest a bloddie Crosse he bore,/ For deare rememberance of his dying Lord. (I.i.2)
Spenser points out the centrality of religion to Redcrosse's life and to his very identity by making an, er, red cross Redcrosse's emblem.
And there beside of marble stone was built/ An Altare, carv'd with cunning ymagery,/ On which trew Christians blood was often spilt. (I.viii.36)
This altar, located in Orgoglio's castle, depicts a fear Christians had during Spenser's time that they would be killed by non-Christians for their beliefs (although Christians had themselves killed plenty of non-Christians during the Crusades…).
[Guyon] wist not whether blot of foule offence/ Might not be purgd with water nor with bath;/ Or that high God, in lieu of innocence,/ Imprinted had that token of his wrath. (II.ii.4)
Evoking the famous image of Pilate trying to wash the blood of Jesus' death off of his hands, Guyon literally can't wash the blood off poor little Ruddimane's hands. Does Pilate's offense seem similar or different to Ruddimane's?
More sweet and holesome [the Bowre of Bliss], then… Eden selfe, if ought with Eden mote compaire. (II.xii.52)
Eden, the Biblical paradise on Earth, was essentially the best place ever. So, by suggesting that the Bower of Bliss, one of the worst places ever, could be better than Eden means that something is very wrong.
So much her malice did her might surpas,/ That euen th'Almightie selfe [Ate] did maligne,/ Because to man so mercifull he was,/ And vnto all his creatures so benigne (IV.i.30)
Hint: you know you're evil when you start picking fights with God. Ate, the sower of discord, is thus officially an Evil McEvilson.
And euer when [Belphoebe] nigh approcht, the Doue/ Would flit a litle forward, and then stay,/ Till she drew neare, and then againe remoue;/ So tempting her still to pursue the pray,/ And still from her escaping soft away. (IV.viii.11)
Belphoebe and Timias are about to reconcile thanks to this helpful little dove. Incidentally, the dove is also a religious symbol of peace and hope in the Bible.
By [Concord] the heauen is in his course contained,/ And all the world in state vnmoued stands,/ As their Almightie maker first ordained,/ And bound them with inuiolable bands. (IV.x.35)
Satyrane describes his almost visionary experience in the Temple of Venus, where Venus is no longer associated solely with love and lovers, but with religious power over the universe and heaven.
[People] liue, they die, like as [God] doth ordaine,/ Ne euer any asketh reason why/ The hils doe not the lowly dales disdaine;/ The dales doe not the lofty hils enuy./ He maketh Kings to sit in souerainty;/ He maketh subiects to their powre obay. (V.ii.41)
Debating with the (pretty socialist) Giant with the Scales, Arthegall appeals to God and religious authority as justification for the inequality in the world.
Well therefore did the antique world inuent,/ That Iustice was a God of soueraine grace… Calling him great Osyris, of the race/ Of th'old Ægyptian Kings, that whylome were;/ With fayned colours shading a true case. (V.vii.2)
In the Temple of Isis, where Britomart goes to receive a vision of her future, we see a vision of non-Christian, pagan religion, like the religion of ancient Egypt, in which Christian values like justice can be expressed even in non-Christian religious terms.
From thence into the sacred Church [the Blatant Beast] broke,/ And robd the Chancell, and the deskes downe threw,/ And Altars fouled, and blasphemy spoke,/ And th'Images for all their goodly hew,/ Did cast to ground, whilest none was them to rew. (VI.xii.25)
This image of the Blatant Beast destroying the objects in a church represents the fear of iconoclasm present during Spenser's time. Iconoclasts, who were extreme Protestants, believed that visual images and objects obscured rather than contributed to genuine religious experience.