Tularemia is the biggest concern. It is more of a problem in warmer states than colder ones. When I was in school taking epidemiology many years ago, Arkansas was the tularemia hotspot of the US. I think there are far fewer cases now as fewer people subsist off the woods.
I used to not worry about catching anything until I got into healthcare and actually started seeing people with diseases from wild animals. I still trap and hunt as much as I used to, but now use gloves when skinning fur bearing animals and small game. I don't worry about deer.
I also try to limit when I contact these small, furry animals to winter time. Hopefully they have less fleas and ticks on them at that time, thereby decreasing the chances of getting something. Chances are pretty low, by the way.
So in answer to your question, yes, rabbits are safe to eat. Take some small precaution when handling them and you will be fine.
