The reason is a lack of user research to understand how people think and act when shopping, and how they navigate their way through the experience to get it done. It's the user experience concept of a mental model, if you want to get fancy, or the application of a system matching the real-world heuristic they teach you about in college.
There are times when going through the self-checkout makes your grocery shopping trip easier. Instead of having to wait in line for someone to help you when you only have a few items in your cart, you can just buzz through the self-checkout line instead.