It really depends on the type of fans dealt with in each fandom. The fandom "war" between Hetalia and Homestuck started on Facebook, when a Hetalia fan made a page saying "Homestuck fans should shut up". Naturally, Homestuck fans went into an uproar, so fans started flaming each other and sending hate.
However, these are only a few fans. Many people love both Hetalia and Homestuck (and they're called Hetastuck fans), and most members of each fandom don't hate on the other fans. Some fans just don't get along with others.