But that's the current primary use case for AI. We aren't anywhere close to being able to sanitise input from hostile third parties enough to just let people start inputting prompts to my own system.

there's a whole world of AI tools out there that don't focus on developers. These tools often need to interact with external services in one way or another, and MCP gives those less technical users an easy way to connect e.g. Notion or Linear in a couple of clicks, with auth taken care of automatically. CLIs are never replacing that use case.