It's quite true that the whole protest movement started out as yet another raid by the #chans, but things changed once Mark Bunker put a video on his Youtube channel saying "Er, guys, knock off the DDoS BS, you're not helping": it happened and led to the movement dispersing, setting up new bases of operation and joining forces with established anti-Scientology voices. In fact the majority of posts on the subject within the #chans now rubbish the whole idea, as it's gone mainstream and thus doesn't fit the "l33t haxx0rz on steroids" image the more pimply-faced, daylight-averse posters like to project. Anonymous is now an entity distinct from the #chans, but irretrievably entwined with them.
While the Rickrolling (also now gone mainstream, but that's a matter for a different post) and meme-shouting do feature at the protests, these seem to have taken on the mantle of acting as a unifying force for what is, basically, a bunch of people wearing masks to protect their identity who do not know one another to get behind and hang their protest off, and there is some pretty creative work being done in welding these into actual protest slogans, activities and chants. In any event, it doesn't seem to matter what's actually being said, as long as it's legal and noisy enough to attract the attention of passers-by, who are engaged by legions of leaflet-wielding protesters who are passionate and articulate about the cause. It seems to work, though the jury's out as to how this is going to pan out in the long term.
If nothing else, the whole thing is a remarkable insight into how the power of the Internets can be harnessed to rapidly create and deploy a huge body of people who are prepared to engage in mass peaceful protest which is at the same time completely without a hierarchical structure.