You can't judge a person's character based upon the outcome of their actions, but upon the intention of the action.
You could argue Dagoth Ur is well-intentioned, from a certain, anti-Empire pro-Dunmer point of view- all he wants is to liberate Morrowind.
It's less about intentions and more about how they go about seeing their intentions fulfilled. A Skooma smuggler who's trying to feed his family is certainly well-intentioned, but his means are not the best, therefore he's not considered "good", but "gray".
The other way around actually. Dagoth Ur the place is named after Dagoth Ur the person. (Lord Voryn Dagoth, Lord High Councilor. "Ur" being the title of the "Lord" of Great House Dagoth)
And he was well aware of the Ministry of Truth hovering over Vivec. Like the Emperor, he has eyes and ears throughout Vvardenfell. While I don't agree with his methods, I believe he cared enough about Morrowind that he would have done something about it once his war with the Tribunal was over.
Dagoth Ur certainly cared about Morrowind, but he was so crazy he likely would have seen the eruption of Red Mountain as "cleansing" out the impurities that the Empire had put into Dunmeri culture- the land itself throwing out the Imperial menace and returning them to the "true Dunmer". As a counterpoint, Azura cared about the Dunmer more than any other god, but she still created a prophecy that ended up with most the Dunmer being destroyed.
Still, the Nerevarine isn't good or evil, it's how you play him. If you were to, say, roleplay a Nerevarine who has read the sermons and wants nothing more than the Ministry to kill everybody, you're certainly evil. If you roleplay a Nerevarine who knew nothing about this event, who only saw the immediate threat, you're good, if a little short-sighted. Arguably, defeating Dagoth Ur is the lesser of two evils, as Dagoth Ur was going to infect the whole of Tamriel with Corprus and turn it into a theocracy worshiping him and/or Akulakhan.