The Faerie Queene has the distinction of being the only character in The Faerie Queene who we never actually meet. This might seem a little bit odd because, as you might have guessed, she's kind of the star. But actually, the Faerie Queene's MIA status adds to her mystique; she always exists more in our imagination, and in the imagination of the other characters, than she does in reality and therefore will never disappoint.
Her ability to have so much influence over the characters and actions of the play without needing to be physically present speaks to the immensity of her power—just saying her name makes us, and everyone else—pause and listen. The Faerie Queene is also one of the most straightforward representations of Queen Elizabeth I in the poem, being a queen and all that.
While Belphoebe is an embodiment of Elizabeth's famed chastity (see Belphoebe for more on that), the Faerie Queene is an embodiment of Elizabeth's sovereignty—her queenly power. As such, it's also safer for Spenser to describe and praise her only from afar, since a bad or insulting depiction of the queen was a one-way ticket to a world of pain (and prison). Therefore, by keeping the Faerie Queene as a majestic idea and ideal, as opposed to an actual person we encounter and critique, he never runs the risk of depicting her in a less-than-flattering light. Well played, Spenser, well played.