What do people expect them to do? Invite the person to the podium to speak into the mic?
My thoughts precisely. If someone stands in a public space with a loudhailer, they have high nuisance value and little else. They cannot be arrested because its a public space - in contrast to doing the same in an auditorium (which, whilst open to the public, is a hired space and noisy attendees can be ejected))
Standing in front of them chanting blocks their impact. Yes, to the religious nutter it will be perceived as an opportunity to shout back, "You're scared of my message..." etc. But what a way to bolster one's sense of being united against a religious opponent.
Of course, they could have ignored him. But they are modelling another type of response. And, honestly, I cannot blame them for forming a blocking wall - I've seen that done in response to the Westboro nutters.