In part it really is an emotional response, which is hard to pinpoint in one place. It's not any one detail -- there's always details that are problematic with any system. I could create a long list of details, and that would account for some of it, but even those cumulative details don't really account for it.
I think it's really a feeling that I am not in control. I don't feel confident about my applications, and the way they will work in production. They depend intimately on a system that I don't understand, that I feel I can't understand. Learning about Zope doesn't lead me to feel more in control -- often it's exactly the opposite, I feel less in control the more I learn, which is incredibly discouraging. And in the end, I simply don't buy the It's Complicated But It's Powerful argument -- not just for Zope, but in an abstract sense I find that argument flawed. Even its "power" feels like a flaw to me, so I'm left with very little motivation.