They should take much mora damage from arrows (they have no armor)
You are forgetting that (in the movie at least, haven't checked the book yet) Legolas shot three arrows in a zerker (Helm's Deep), but wasn't able to kill it. He still blew up the deeping wall. So they aren't as vulnerable to arrows as you think they are.
(Ofcourse the problem of the unkillable zerker was quickly solved, he blew himself up soon after )
So my guess is the problem lies with the ents