Perhaps I’m not the best person to offer advice on how to deal with trolls. My site gets relatively light traffic, and the people who visit tend to be way too polite, nice, or otherwise supportive. My lack of popularity in a sense has shielded me from the kind of criticism you’re regularly subjected to. Still, I feel I understand why your positions have been so vilified, and why you often find yourself outside of what the ‘atheist mainstream’ believes.
First, while I think you’re a great writer and I endlessly enjoy your prose, you don’t exactly speak the way regular people do online. Your style is more reminiscent of newspaper editorials than blogs, and in a sense, it lacks a feeling of genuineness. It almost makes one feel as though you’ve been too careful with your words. A little candidness goes a long way online, especially when you’re trying to express frustration.
Second, your controversial position on things is so nuanced, it’s difficult to actually represent it well, especially when one considers the short attention span of the Internet (I bet only a fraction of my readers will even bother to read this entire article). Even when you provide resources to properly analyze your belief, (like the link you said justifying torture that I’m still wrestling with) you’re asking what is essentially the laziest generation in the history of the planet to studiously research your position. That ain’t gonna happen.
Third, you must chose your battles. While you are undoubtedly more recognized than PZ Myers, the man has established a large online following; one that I wouldn’t dare anger. This is not a place I normally expect civil debate (and I don’t actually think it’s the intent of the site anyways). Holding PZ responsible for the things his fans say suggests the solution would be either censorship or policing, neither of which I think is a good idea.
Fourth, your experiences with a psychedelic drugs will always make you an outsider. America is so afraid of drugs, it would rather jail a huge segment of its population than allow adults to make their own decisions about their bodies. You and I both know a prohibitionist attitude is religious in nature, but it has been ingrained long enough in American culture that the default stance on recreational drugs is “drugs are bad, m’kay?”, regardless of religious affiliation.
Last but not least, your criticism of Islam will always be mistaken for racism. I know, because I get the same look from people when I say something. This vile religion has managed to convince everyone that belonging to their group somehow makes one part of a ‘race’, and criticism of this misogynist, violent culture amounts to being a modern day bigot. That’s not a label anyone enjoys, and people are willing to ignore reality if it means they won’t look bad, even at their own detriment.
I know the Internet can be a harsh place, and it lobs criticism far more than praise. Just remember that so much of the Internet is the raw, unfiltered thoughts of people who have no responsibility for the words they say. Take it with a grain of salt, man.