Occurred to me:

Try any Civilization game. In that game, rebels are not what you want to have in your empire. (Civil disorder is a thing; if the population is unhappy, the city will riot and stop producing things.)

Space Empires like Civ, also has rebels. And sometimes you just get an event card that says, "Planet X decided to form it's own coalition".

I suppose in most Age of and Caesar games, rebels are also bad.

Depending on the side you take in the later Geneforge games, who is a rebel and who is the empire is a matter of a choice.

Apart from these two considerations, I guess most games also want the players to feel more heroic by having them beat the odds, being part of a smaller group that is fighting the power, instead of just belonging to a majority force that is more powerful than the opponents right from the start (possibly even without the players' involvement). So for the players to feel more important, the opposing rebel group would have to be better equipped than the government in order to pose a serious threat, and I can imagine that this would quickly lead to the tables being turned, the rebel force seizing the power and the supporters of the former government becoming rebels themselves (making the rebels good again).

I'm not that into Star Wars, so excuse my ignorance, but isn't that what happens there, too? Are there no games that take place during those periods when the Empire to be is still fighting the Republic, as evil "rebels"?

Good point. It's like how people say you can "punch up" but not "punch down." A privileged young man making fun of of a challenged young woman is seen as horrible, while the opposite is often totally accepted or praised. That feeling might transfer to games; i.e. you don't want to feel like like you're punching down at the little guy, but punching up at the powerful.

if you think about it, e-mail can not travel faster then light, so if they need the message to go faster (after all, there are light years between stars, so if I send a message it will take years before it arrives) they need to use a physical ship with FTL engines to carry it. In that case it makes sense.

The Witcher 1 lets you decide to side with or against the Scoia'tael (the rebel faction).

[spoiler]Red Faction 2[/spoiler], though it's pretty lame in its execution.

Pretty much every game featuring the roman empire, though the rebels are called barbarians (= meaining bearded unwashed people).

There really isn't such a thing. These terms are only relevant in the context of perspective. Someone mentioned it unove as well, freedom fighter/rebel from the perspective of supporter is terrorist from the other perspective. These are also inflicted by the winner of such occurences, Rome fighting the barbarians is a good one, or you could say Rome bringing slavery and ethnic cleansing from the other point of view. History and politics are both lies and there is no such thing as right and wrong, noble ideas and such like, there are only winners and losers.

To add, long live the dark side!

I think I accidentally started a geek fight. XD

I would have to argue that there isn't common decency or sense. There is some compassion for the week sure, however a lot of that is driven by the moral tax brigade called charity. There is however common lowest denominators which is where stereotypes and such like come from, it one groups "decency" is another groups "freedom". And there really is no argument for "sense"!

Every single American Civil War game.

Archimedean Dynasty, does it count? I don't recall if it had any established civilization lead by some, but at least there were different factions that tried to stir trouble, like those religious zealots or what were they.

I recall the main baddies in the end though were some (underwater) alien race, but I guess they are not considered as "rebels", simply a threat to everyone's existence.

EDIT: The Mobygame's page explains AD's world in more detail, but not mentioning those zealots or aliens:

http://www.mobygames.com/game/archimedean-dynasty

In Dragon's Dogma the Salvation cult are basically rebels and they are evil. Sure, the government they rebel against isn't exactly good either, but that doesn't make Salvation good in any meaning of the word. They are rebels who try to destabilize human society to speed up the destruction of the world. Definitely evil.

Syrian Warfare.
Rebels attacked Syria. You help Syrian government to fend them off.