Anonymous is not an "Anti-Scientology" group as the author of this article puts it, which may explain your confusion as to why Anon's were present at this particular protest.

Anonymous is the physical manifestation of the Internet. We are everyone, and by our nature, noone. We have no leaders, no organisational structure, or directing command of any sort. The Cult of Scientology became known to us due to the large amounts of information on the Internet pertaining to their abuses and the vast unknown hordes that are Anonymous rose up to challenge them.

However, by our nature, we are do not hold the Church of Scientology as the exclusive recipient of our attentions. Any Anonymous may do what he or she thinks is best for Anonymous