Not always the case IMHO. Take the Dark Brotherhood quests in the Elder Scrolls games for example.
Or an evil party in Baldur's Gate.
That being said...
I had the same problem with the Mexican section of Red Dead Redemption. I was playing this "rogue with a heart of gold" type cowboy for the first part of the game, but then you go south of the border.
In Mexico people live in misery but you can't help them. The game forces you to follow orders from corrupt government officials, torching villages and arresting/killing "rebels".
When you're finally allowed to switch sides and join the revolution it turns out the leader of the rebellion is just as bad as the guys you just helped overthrow.