Adam Jacob's recent essay really makes me think there's no common ground. Attack away if that pleases you, but framing an attack (and a poor one at that) in the language of conciliation reveals nothing but intellectual and moral bankruptcy.
But maybe there is some common ground we can reach with theists.
First, your private religious beliefs are no one's business but your own (and those you freely choose to share them with). The emphasis here is on private. No atheist is, as far as I know, interested in invading your church, your home, your bookshelf or your mind to root out beliefs we disagree with. (And if any atheists do advocate such measures, directly or indirectly, I will add my unqualified condemnation.) Private doesn't mean "shut up", it just means outside the government and mechanisms of social compulsion. It's not enough to just say that "there is no compulsion in religion," you have to actually live it. If most religious people did live that motto (and took the lead marginalizing religious compulsion and privilege), I would be completely satisfied, as would, I suspect, most other atheists, militant and Gnu.
Second, it is manifestly true that religion is not all bad. Religion does not turn people into monsters. Religious people over the years have come up with a lot of good ideas, and sometimes their religion has motivated and supported those ideas. And of course modern Western culture has substantial roots in religion, especially (but not exclusively) Christianity. Similarly, atheism does not turn people into monsters; a lot of atheists and those indifferent to religion have come up with a lot of good ideas (some motivated by atheism itself), and modern Western culture has substantial roots in secular, scientific thought. We can live together in a truly pluralistic culture.
Third, there's nothing wrong per se with making your private beliefs public. Privacy entails that it's your choice what to make public. Restriction on expression is just as inappropriate as compulsion. Of course bringing your private beliefs into public expression means you're now in a context with more subtle and complex rules, but these rules are pretty well-defined. We all talk freely about our opinions, and only the quality of the opinions are legitimate topics for criticism. It's out of bounds to condemn someone directly for the temerity of actually expressing an opinion without regard for its content. There are subtle, unavoidable forms of restriction and compulsion in public discourse (no one wants to be thought a fool or a knave), but those subtleties apply to any topic. We all have to just deal with it.
As best I can tell, the common theme of the Gnu Atheists is to remove all compulsion and privilege from religion. We want, I think, to make religion a truly private matter, just as private as people's taste in music. We don't, in theory, mind churches any more than we mind record shops, so long as both pay their taxes and obey the zoning regulations. Privacy and pluralism is our common ground.