I may be repeating some of the comments posted above, but having been away for a while have only now read this response, and would like to comment in any case.
First, I found nothing in this response that would have led to people to respond differently had they done more research. So far as I can tell, the facts, as presented here, are essentially the same as when originally presented.
Second, though I appreciate the explorations into sharing use of the term, I do note that continued ownership of 'Web 2.0' in the context of conferences is asserted, and hence that there is a sense in which others would not be permitted to use the term in that context. So the original position that prompted the outrage remains unchanged.
The problem in this instance is not so much with O'Reilly and its partner, CMP, as it is with trademark law, which allows companies to take terms already in use (as Tim said, it doesn't matter whether there was prior art) and claim them as identifying marks. And certainly part of the appeal of the term 'Web 2.0' is that both the terms 'Web' and '2.0' were already in use. The traemark, in this case, draws on very public property to create private property.
Still. Though trademark law allows that practice, and though that practice has become commonplace (after all, CMP 'routinely' files trademarks), it seems that the application of the trademark in this case should be subject to some criticism.
First, it should be clear that had either O'Reilly or CMP been open and honest about the status of 'Web 2.0' as a trademark, it would not have been as popular as it became. It is one thing to say that the meme ran out of control, and quite another to have deliberately let it run out of control under false pretenses. The submarine nature of this trademark is probably responsible for as much of the vitriole as anything else.
Second, a trademark may be filed in order to prevent other people from stopping you from using the term - that is at least part of the basis for the trademarking of Wikipedia and Apache. Proponents of 'Freenet' know what happens when a company comes along and trademarks your name out from under you. But there is a very big difference between this and using a trademark to prevent anyone from using the term at all (in this context).
While I do not condone the tone of many of the comments, I remain, after Tim's post, sympathetic with them. The public was misled, and what was commonly believed to be a term anyone could use, was revealed after the fact to be private property, and moreover, property that would be (and may still be) enforced with lawyers' letters.
I believe that this issue is a long way from being resolved, as the continuation of comments two weeks after the reply suggests. I am certainly not satisfied.