Bunny faunus with human ears:
[img]http://vignette3.wikia.nocookie.net/rwby/images/2/2f/Vol2_Velvet_ProfilePic_Normal.png/revision/latest/scale-to-width/250?cb=20140926074035[/img]

Wolf faunus with human ears:
[img]http://vignette4.wikia.nocookie.net/rwbyfanon/images/0/02/Gary_Gray_White_Fang.png/revision/latest?cb=20140620000115[/img]

Just because the faunus might have animal ears doesn't mean they don't have human ears. It's actually a very common precedent in genetics, organisms evolve with a new organ or something to do a better job than the old one but the old one takes another three thousand years to be edited out of the gene pools. Maybe faunus in three thousand years will have cat ears but no human but they're not like that now.

Plus you'd just look really creepy without ears.