The cost of a single MCU with 128kB of program space and 4kB of RAM space is about US$10. This is dirt cheap, even when compared to low-end SBCs. However, a single MCU (as a chip) doesn't do much. You'll need some external circuits and a circuit board to use an MCU in an application.
Depending on what you need to interface with, the add-on circuit can be inexpensive, or very expensive. To compare to a ``typical'' SBC designed for embedded control, let us use the following components:
The circuit board can be as simple as a breadboard, or a custom PCB. We'll just say it costs US$10. After adding all the costs, a function circuit board based on an MCU is about US$20. With volumn discount, it is likely to reduce the cost to less than US$10. This set up is comparable to an SBC that costs easily $75 or more.