All books are biased. Just like in real life. That's part of what makes TES lore so rich. In a D&D game, you read "orcs are evil barbarians" and that's the http://tvtropes.org/pmwiki/pmwiki.php/Main/WordOfGod. You can't have an orc that is a good barbarian or an evil bourgeois.
In TES, you read "orcs are evil barbarians" and that's just the fictional author's bias. Sure, many orcs are aggressive barbarians, and they're not liked by most other races. And they were still officially considered as monsters by the Empire. Doesn't mean they actually are monsters; and indeed you get to meet many orcs which simply aren't evil at all.
The Dunmer have the most sinister reputation of all races, what with their legal practice of slavery and assassination and their open worship of three daedra (though the Tribunal Temple has cut down on this later point as strongly as it could). In fact, you'll find in Dunmer culture many of the elements that defined the Drow in D&D, the aforementioned slavery and assassinations, the oppressive strength of the clergy, the fascination with creepy-crawlies (though it's scarabs rather than spiders), and even originally the underground part, as at the height of its activity the Red Mountain was constantly covering the land with a ceiling of smoke making the whole province look like it was a large cavern.
But it is so much more than that. Because it's been fleshed out in a way that makes sense and the Dunmeri culture has reasons for its aspects others than simply "we're evil, bwahaha, let's go kick puppies to prove to the audience that we're evil."
The Dunmer, simply put, became realistic people. So, sure, many of them are still bastards. But not all. And they're bastards to varying degrees. It's possible to empathize with them. And the other races do not appear to be really that much better than them. There are good and bad people in every bunch, no clear-cut black and white with the dark elves as all bad.
The Dwemer most certainly weren't evil. Frightening, blasphemous, yes. Evil? The only places where they're shown as being cruel is in the Sermons of Vivec, where they capture and vivisect Vivec's mother by curiosity, and one of Marobar Sul's pieces where the editor's note make it clear that the text wasn't actually about Dwemer originally, but about Dunmer and it was adapted to not displease a Dunmer audience.
One of the ways I think about the dwemer, is to think about them as if they were actually extra-terrestrial aliens. (They WERENT, but their culture was alien enough that they might as well have been.) Imagine if energy beings from the 16th transcendent universe suddenly popped out of a big glowing thing, and took up residence on the earth, and went about trying to prove that our universe was false, using sciences and principles that simply dont exist naturally in our universe (but do in theirs)-- and that they live next door to you.
They make wonderous and strange devices which defy rational explanations, and do some very odd things which we consider abhorrent, frightening, or terrible--- but they are not concerned with them, and treat them as part of every day life, like eating, sleeping, or going to the bathroom.
People will naturally be distrustful of them, spin wild stories of how they use their technologies and knowledge in ways to secretly wish to enslave and torment everybody, despite a lack of evidence. The innate alien nature of them will make it difficult for them to set the record straight, as their accusers would simply say that "OF COURSE they DENY it!", and the like.
The reality is that they are people, just like you--- Just "Different," and with different perspectives and mores.
Were they evil? Certainly not. Was what they were doing potentially cataclysmically dangerous for the mundus? Oh, most certainly! Were they strange and alien beyond the comprehension of their peers? For a certitude.
To a person who considers the mundus to be a nice, safe, perfect, and wonderful creation made by the gods out of love for their children, what the dwemer were up to would have seen utterly horrible; Like other Mer, they wanted the current, faulted world GONE, and wanted no part of it. They saw nothing wrong with trying to destroy it, and escape. Many people consider a desire to destroy the world to be a sign of being sadistically evil-- Especially when there is a lack of concern for the other people who live on said world. The reality of the matter, is that the dwemer felt that destroying the mundus would be a good thing for EVERY aspect trapped inside it, and NOT just themselves.
So, were the dwemer would-be saviors stopped by a daedric plot? Or were they sadistic crazies hell bent on destroying the world who's plans were righteously foiled by heroic champions of the divine?
Both are true.