I am not sure what you mean by 'supposed to' agree to the license. You are correct in that the license doesn't self-enforce, but legally you have agreed to follow the license when you download the code. So, Apple can take legal action to enforce compliance with the license, which is what they did whey they sent a C&D notice to f.lux.

A license can restrict non-commercial purposes, too (as long as they aren't purposes protected by law, e.g. fair use). While it is true that most companies only go after license violators who are using the software for commercial purposes, that is only for practical reasons, not legal.