The circle of the heretics in Canto VI is indeed generally very weird. One would expect Dante, a pious Catholic poet, to put in Dis all the great heretics of the early church (Marcion, Donatus Magnus, Arius and Nestorius) and the Cathars (some of whom still wandered around Southern France in Dante's day), yet they are not mentioned anywhere. Instead, Dis is inhabited by the Epicureans (put there by Dante because they denied the immortality of the soul) and three imperialist figures - Cardinal Octavian (appointed antipope Victor IV by Frederick Barbarossa in 1159), Farinata degli Uberti (the leader of the Tuscan Ghibellines who defeated the Florentine Guelphs at the battle of Montaperti in 1260) and Frederick II.

The thing to bear in mind is that Dante's thought does seem to have evolved over the course of writing the Commedia. Many scholars, such as George Holmes in "Dante" (1980), have argued that the most probable dates for the writing of Inferno were 1304 to 1308. This would mean that he wrote it before Holy Roman Emperor Henry VII's expedition into Italy, which sparked a great Ghibelline revival in Lombardy and Tuscany that Dante was certainly affected by when he wrote Purgatorio, where in Canto VI he more clearly displays imperialist sympathies in his nostalgia for the Augustan era Roman Empire and his criticism of Henry VII's predecessors Rudolf and Albert of Hapsburg (the Commedia is meant to be set in Holy Week 1300, 8 years before Count Henry of Luxemburg was elected King of the Romans) for staying put in Germany, rather than coming down to Italy and sorting things out. Dante's imperialism is even more clearly displayed in the letters he wrote in 1309 - 1314 and in his political treatise Monarchia (1314), but there's no trace of it before 1309. Dante is certainly very critical of the papacy in Inferno, anticipating that Pope Boniface VIII (died 1303) will go to hell and condemning the Donation of Constantine (the Carolingian forgery that gave the Catholic Church temporal authority in the Western half of the Roman Empire). Yet Dante had personal reasons to dislike Boniface VIII, since he played no small role in the coup of the Black Guelphs in November 1301 that led to the White Guelphs (the faction that Dante belonged to) being exiled from the Republic of Florence in January 1302, and his criticism of the Church owning property and meddling in politics may well have been influenced by calls from the more radical Franciscan friars for the Church to return to apostolic poverty - the Franciscans were a big force in Florence, having a huge basilica and friary at Santa Croce since 1294. It thus seems most likely that at the time of writing the Inferno, Dante was still just a disaffected White Guelph who was becoming increasingly disillusioned with republicanism and the world of the city states, paving the way for the imperialism he espoused from Henry VII's arrival in 1309.

As for the specific reason why Frederick II is in hell, some historians, such as Alexander Murray in "Reason and Society in the Middle Ages" (1978), argue that it was because Dante believed that Frederick II had once declared that nobility lay in good birth and ancient riches, a statement with which Dante vehemently disagreed as Dante's own view was that nobility lay in personal virtue (an almost meritocratic ideal).