Like the threats of violence endured by people trying to attend the ACL meeting? It's not illegal to be Christian but it is illegal to threaten violence against them. Sadly the coppers are more likely to take action against the lone Nutter than the groups that threaten violence against those attending the ACL meeting.
I assume you're referring to what happened at the Arrow hotel in Melbourne yesterday? After reading the only two articles published about that (which came from News Ltd sources so reading through the obvious bias) the difference was that the protestors at the ACL meeting were rallying outside the meeting with the police in attendance to ensure safe passage for people going in and out of the hotel. There were no reports of arrests so I assume that the police were satisfied the behaviour of the protestors didn't constitute a crime.
The supposed "threats" were comments on the hotel's social media page from people saying they would boycott the hotel for hosting this event. That is a legitimate form of protest. Not what the pie thrower did, when he committed a clear public act of assault.