I think this goes back to the philosophical debate about adblocking that won't be over anytime soon... and I'm firmly on the side of the user retaining full control over the content he/she consumes, which in some ways is equivalent to the freedom one has to close his/her eyes or look away at something else, and believe that technological measures like ad-blockers are a way of protecting this freedom.
The alternative, which advertisers would very much like to happen, is for even those basic freedoms to be taken away; for users to essentially be forced into consuming whatever content they desire.
I think it's pretty easy to draw a distinction between blocking ads for personal convenience and replacing ads with other ads for profit.
The only site owners who aren't hurt by this type of malware are the terrible ones with no regard for their users, who are willing to double up on now many popups they slam the visitor with, or ironically even willing to join shady pay-per-install malware networks just to get their revenue back up to normal levels.
I'd like to believe you've never run a site before, because otherwise you'd have an idea of just how expensive it can be.
The only site owners who aren't hurt by this type of malware are the terrible ones with no regard for their users
...or the ones who don't put any ads on their site? I do happen to have such a site, and the reason it doesn't have any ads is because it doesn't need them.
In my experience, the most ad-filled sites also tend to be of the content-farm type, providing little in the way of quality content.
See my billboard example reply to the comment above to see why I believe that Privdog and Superfish are run by thieves.
It's a clear theft - a malicious third party that intercepts money exchange between two other parties without knowledge or consent of either.
Is it a crime for someone walking around to not look at a billboard? Of course not.
Is it a crime for someone to plaster over an ad on a billboard with their own ad? It isn't explicitly theft, but it is certainly a crime, and the end result is nearly the same (in the meatspace example it is the advertiser that gets the shaft, and in the digital example it is the billboard maker that gets the shaft).
Privdog only replaces ads on the machine on which it is installed, and those who don't have it installed will see the original ad. The meatspace equivalent would be something like an augmented reality device that replaces ads for the one wearing it; and this is not a new idea, although no one has wanted to replace ads with other ads: