'Passed', to me, has religious overtones. It suggests, to me, a passing from a mortal coil to an immortal one, or something of that nature. Speaking of death, dying, of someone who has died, seems much more accepting of an end of an individual's (animal, plant, whatever) life. Which, to me, is what it is.
Before anyone thinks I'm being critical, read what I've said: I've talked about what certain expressions mean to me. I haven't mentioned anyone else. Other people can think, and say, what they like about death.
I'll continue to say that someone or something (like a tree, for instance) has died. Death gives life anyway. When you're as close to nature as I am, you see death as a giver of life to other organisms. See what I did there?