The ad injection the article refers to is related to Chrome extensions/desktop malware modifying unrelated page's HTML content to inject ads (such as, you go to
http://example.com, which may have no ads, but some local software on your machine/web browser alters the HTML to add their own ads to the page you're visiting).
The only ads I've ever shown on the site are through Google AdWords, and while Google isn't the greatest in regards to privacy, as far as I've had the site, I haven't come across a breach or news article that alludes to any of their ads having been compromised as an attack vector (it's likely the safest/least compromised ad network out there).
As far as running a 'for profit business' - that's laughable, as the revenue from ads does not even come close to covering the hosting + my time spent on the site (especially considering I have been pretty inactive on p99 for awhile now, but kept the site up for the player base).
The great thing about FOSS/open source software (which is what anything I create is) is that you're free to fork, modify, extend and run your own instance of it if you like (just note that the log uploader is GPL, so you have to release the source if you distribute the binary modified, and the site code is AGPL, which means any portion of the site you modify would also need to have a link to the modified source available).
Lastly, I really appreciate what the p99 developers have done with the server, but it is a bit of a laugh for you to complain about me making any revenue off "other people's hard work", when the server itself is just that (a derivative of other people's hard work - that being the original EverQuest project).