The Faerie Queene is a strongly Protestant work in which Spenser intentionally incorporates his own beliefs into the Story. What has made the poem popular among readers of all faiths, not just Protestants?
While Spenser spends a good deal of time attacking the Catholic Church, he makes it clear that there is a greater overall evil that threatens mankind, the very basic evil of sin. This is the dragon that Redcrosse defeats at the end of Book I. By broadening the battle to good versus evil, the spiritual part of man's existence, Spenser expands his audience far beyond the narrow range of Elizabethan Protestants.
What is Spenser's view of pagan (non-Christian) virtue? Does it have any value to him?
Yes and no. Spenser is quick to recognize that native virtue (as usually represented by forest creatures or people brought up in the forest) is oriented toward the good. By comparison to the many perverse characters in the poem, this is commendable, but it pales in comparison to the virtue of the Christian heroes. Natural virtue is good as a building block toward the true religion, but if it falls short, it is worthless, mere idolatry.
In what ways are the stories of Redcrosse and Britomart parallel?
Superficially, they are hardly parallel at all; Redcrosse goes through an arduous process of discovery and cleansing until the final dramatic showdown and glorious victory, while Britomart pops in and out of the narrative, helping out here and there, but never, it seems, getting any closer to her goal. But on the level of the allegory, both stories elaborate on a virtue, instructing the reader how to recognize falsehood or insincere chastity, until the virtue is mature and can conquer true evil. In this respect Book I and Book III have a similar buildup and climax, despite the obvious difference in plot.
What is Spenser's view of "courtly love"?
Courtly love is the love of Arthurian romances and their Italian counterparts, sources that Spenser used extensively. However, he tends to represent courtly love as superficial and even silly, a far cry from pure Christian love. See the ridiculous task that the Squire of Dames tells Satyrane he must perform for his lady (III.vii.53-61)--such devices were common to courtly love stories, and Spenser only mocks them.