I completely agree that there are some issues with anonymity, but I think overall this is about as close as a person can get to anonymously earning / trading / spending any sort of currency.
What we all have to keep in mind is that we're in the midst of a grand experiment and, for a thousand reasons, we have to accept the possibility (however remote) that it could fail. Heck, the wiki comes right out and says so numerous times.
Having said that, I'm not heavily invested in BTC because my mining capabilities and investment resources (aka evil American $) are quite limited. But I'm confident enough in the concept that, if I did have the option to invest more, I would. All the same, we must keep security, including anonymity, a top priority as Bitcoin grows.