Will rabbits come out of their hole on their own?
Rabbits will venture out of their holes, despite being scared into them.
Alternatively, if you're impatient, you can use a shovel to dig up the hole, forcing the rabbit out. However, this has the negative effect of there no longer being a renewable source of cute little critters for you to murder in your quest for survival.
It's worth noting that holes will continue to spawn rabbits even if you successfully trap one at that hole. This will allow you to reset your trap on the same hole after catching one.