An end-user running an ad-blocker has literally nothing to do with the appropriate role of the infrastructure provider (which many argue should be an unbiased plumbing system).
I do think there are some ethical concerns for running an ad-blocker, but I don't think this is one of them.
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
I 100% support the right of advertisers' content to be handled with the same diligence and priority as any other source on the Internet, without blocking or throttling at the ISP layer.
I 100% support my right to choose, filter, and select what legally-entitled content I download from the Internet, using whatever mechanism I see fit. If a page redirects me to a freely distributable copy of "Pixels", I'm not going to use my network resources to fetch it just because I can. That content doesn't interest me and I don't want it. Well, same with invasive advertising: I wish not to use my paid network resources to download it.
Your statement is the equivalent of "how can you support telephone companies acting as common carriers, but still think it's OK to hang up on telemarketers?" It's a non-sequitur.