There's nothing good or moral about a serial killer. What Dexter does is murder, pure and simple.
Dexter is little different than the guy who pulls the switch or injects the poison into a death row prisoner. They perform murder on a regular basis and even get paid handsomely for it.
With a few exceptions, Dexter goes out of his way to make sure his victims deserve what he does to them. Again, it's no different than the legal system. We only deem that
acceptable because, honestly, we have no real choice in the matter. Whether there's a judge, a jury, or a random shootout on the streets that kills innocent bystandards, it's all the same in principle. Dexter simply doesn't follow those
And while he's also a serial killer by definition, he doesn't target
random or innocent people. There's a huge difference, which is exactly why he's so much easier to sympathize with as a character.