While we're not going to say the tone of The Faerie Queene is never humorous, outright silly moments are few and far between. And it's (probably) not because Spenser didn't have a sense of humor, it's that he's writing in a tradition of epic poetry in which heroic action and heroic quests were taken very seriously. Check out this seriousness:
Of all Gods workes, which do this world adorne/ There is no one more faire and excellent,/ Then is mans body both for powre and forme,/ Whiles it is kept in sober gouernment. (II.ix.1)
Wow. We definitely sat up a little straighter after reading that. We have to keep our "sober gouernment" up and running.
Spenser is imparting some major wisdom that he wants to encourage his readers themselves to take very seriously. We see even represented within the poem that characters who joke around constantly or prioritize "fun" over duty tend to get themselves into trouble. The seriousness of tone is related to the poem's elevated tone, by which we mean a tone that gives an impression of dealing with topics and subjects of great importance and distance from day-to-day life.
Spenser doesn't just want us to take his moral lessons seriously; he also wants them to be respected as something extremely important. Indeed, drawing his reader's attention to the meaning of values and virtues that we might just think of vaguely without great detail is kind of the point of the whole poem. Allegory, combined with this serious and elevated style, allows Spenser to investigate and describe in great detail the inner workings of concepts that we otherwise might take for granted.