I am not treating all net traffic equally, I'm not visiting at least 99.99% of global websites - and that is perfectly consistent with net neutrality.
In that sense, an ad blocking or extra-ad-adding service that is implemented against my wishes by any third party (no matter if it's ISP, software vendor or someone who hacked my computer) violates that neutrality, but the exact same ad blocking or ad adding done by me or the content provider is acceptable.
Here's an article by Tim Wu, who coined the term explaining that he is specifically talking about public network neutrality and common carrier laws: http://www.timwu.org/network_neutrality.html