I'm an embedded developer, and I've recently started teaching a coworker about microcontrollers. I think it's most helpful to first understand the basics of digital electronics. Transistors can be wired together to create logic gates, and logic gates can be wired together to create flip flops. A flip flop can be thought of as a single bit of RAM. Logic gates and flip flops can be used to create all sorts of useful circuits like counters, shift registers, adders, multipliers, multiplexers, etc.

With this foundation, one can understand a microcontroller as a big digital circuit. A CPU executes instructions by using a digital circuit. The instruction's op code is selecting the appropriate circuit to operate on the instruction's operands. Microcontrollers also have peripherals like timers, serial communications (spi, i2c, uart), and analog to digital converters. All of these are digital circuits that are configured by writing bytes to registers. Those registers can be thought of as the inputs and outputs of those circuits, just as if they were built with discrete flip flops and logic gates. In fact, many microcontroller datasheets provide diagrams of the logic circuitry for these peripherals.

Once you can truly understand how the hardware operates, writing the code to configure and operate that hardware is pretty straightforward.