Was the Master evil? That's a pretty easy question to answer, I think. The Master wasn't evil, he was insane. Back when he was Richard Grey, the Master--as I'm sure we're all aware by now--was dipped into the F.E.V vats and horribly mutated into the thing we see in Fallout 1.
We already know that it changed how he looked and thought, but really think about how it must have felt for Richard to be turned into a mutant; imagine the pain of your body melting for a straight month, alone, knowing that everyone else you were traveling with was dead. I doubt he knew that Harold survived, but I doubt it would be much of a comfort regardless.
Eventually, Richard's... well, blob, began to expand--to devour everything that was alive to give itself mass, and in doing so not only was Richard absorbing their bodies, but their minds also. If he wasn't driven insane from the F.E.V, than adding an untold amount of other people's minds to his own surly would have done the trick. Their own fear and anguish at their deaths were likely added to his own pain, again and again.
Once he started calling himself "Master", it was game over. I'm pretty biased here, and this is just my silly opinion on the matter, but I think feeling that horror every time he absorbed someone was what sparked the "Unity" idea. Humanity was weak, alone, and afraid. It was dying out one by one, yet he was a being that could not only save them, but make them better.
It worked, kind of, but we all know where the massive flaw in his plan was. He genuinely believes that what he's doing is for the sake of humanity, that by turning everyone into Super Mutants he's ensuring his species will survive. He even cured Cancer in the process!
Plus, if you can make him realize that the Mutant's are fertile. he gives up. He sees that everything he's done has, ultimately, been for nothing; the human race wouldn't be able to populate if his plan worked, and as I said, everything he's done up to that point was for mankind.
Personally, I find the Master to be one of the most tragic characters in Fallout. He did horrible things for the right reasons, and when presented with evidence that it was all for nothing, he loses the will to keep going. The weight of what he's done, the knowledge that all the lives that were lost because of him died for nothing, drove him to suicide.
Master was not evil, he was simply driven insane by the horrors of the wasteland.
