If the internet lowers the barriers to (by reducing the transaction costs of) the kind of free speech that marks a healthy public sphere, it should come as no surprise that it has the same effect on speech we deplore. The internet isn't a freedom-and-democracy machine; it's a communications medium. It makes possible a greater volume of communications of all kinds. Its capacity to foster collaboration and collective action makes no distinction among the purposes of the collaborators and actors.
The same, of course, is true of print. But the internet has made the volume of communication and the ease of collaboration and collective action so much greater that we find ourselves in a new landscape, with new challenges and new dangers. As Shirky says in Here Comes Everybody, "more is different."
No one can predict with certainty what the result will be. What we can say with certainty is that we're not going back to the old landscape. So our best hope lies in fully understanding how this new communications medium works, and in finding ways to promote and foster the social practices arising from the medium itself that are most conducive to a healthy public sphere.
The "YouTube Smackdown Corps" watchdog movement described in the Times article operates in much the same way as the Wikipedia community, which is large and vigilant enough to reverse most Wikipedia vandalism in short order.
If Shirky's contention in the Foreign Relations article is right, this kind of action — a version of "publish-then-filter" — will likely prove more effective, in the long run, than straight-up censorship.
And this, too, is worth noting: If the ability of terrorists to use the internet as an organizing tool scares us — and I think it should — then it hardly makes sense to say that the organizing capability of the internet is irrelevant, or only marginally relevant, to movements for democracy. Again, the internet isn't intrinsically a power for good. By what logic would we regard it as powerful only when the people using it are bad?