""Should the civilizations of man, elves, dwarves, and other such allied peoples be civilized and should they represent those ideals and principles generally considered to be 'good'"?"
If I'm running Tolkienesque High Fantasy then the protagonists' side is Good, and the enemy is Evil. If I'm running Swords & Sorcery then the protagonists' culture may be pretty Bad, but any enemy culture is still probably more Evil.
My campaigns (and it's all my version of Greyhawk) are somewhere between the Tolkienesque vision and a Wilderlands of High Fantasy sort of setting.
The main human country that matters in my campaign -- Bissel -- is mostly Lawful Good in its upper leadership, but men are men, and some of the nobles are self-serving or incompetent. Among the commoners, there are lots of good people (Pelor, St. Cuthbert, and Rao are the most popular deities), lots of neutral people (Obad-Hai and the "Old Way" are also popular), and a fair number of evil folks too -- ranging from bandits and thieves to evil cultists. There are no serfs or slaves, but the rich are much richer than the poor, and it's by no means a democracy. It does have "rule of law" though.
Bissel is at war with another human country, Ket, whose leadership is Evil. Their common people run the gamit, but the Evil of Ket is about it's alliance (an open secret) with Iuz, an Empire run by an evil demigod, and their use of humanoid mercenaries as regular and werewolves and bandits for infiltation/terrorism. Social classes and rule of law are similar to Bissel.
Another human society one party will gate to soon is Cauldron, from the Shackled City Adventure Path. In my version, Cauldron is like the Old South. The rulers are plantation owners, and the wealth of the city is built on slave labor. We'll see how the party reacts to that, but it's still better than the alternatives from the Monsters, with the two strongest factions in the region being cultists who want to destroy the city in a volcano and start Hell-on-Oerth and true ghouls who want to kill, reanimate, and enslave EVERYONE.
So how are the humanoids different from humans, elves, and dwarves?
Elves are almost always Good (except the Drow, who are almost always Evil), but many are isolationists. Dwarves are generally Good, but many are greedy. Halflings are generally good, but some steal.
Among the humanoids, orcs are usually bloodthirsty savages, some of them bred for war by Sauron (who exists offscreen in the distant West) and Iuz. But one group of PC's recently met a group of neutral orcs, who worship and Cave Mother, are led by females, and just want to be left alone (the PC's cut a deal with them).
This same group earlier befriended Meepo the Kobold and helped him become ruler of the Sunless Citadel, with a mutual leave each other alone pact between the Kobolds and local humans. Whereas most kobolds are just evil trapsters and ambushes.
Many goblinoids belong to a secret society (the Red Hand) that's building an army to invade and destroy the human lands, to pillage everything and eat the survivors, just because "they're @@@@s like that". But one part of PC's met a goblin king in the Caves of Chaos who, while LE, was tired of fighting the humans and made a deal for peace in exchange for a cow a week -- essentially, these goblins are on a reservation.
Other humanoids and monsters like Dark Ones, Illithids, Duergar, True Ghouls, Drow, all have their own agendas, which generally involves killing other races and looting them, or surviving against others who try to do the same to them.
So is human society good? Some of it is, some of it isn't, a lot of it is neutral. But mostly, it's just a whole lot better than Monster society. You might not like everthing about the human society, but you'd be dead in the Monster one.