Reddit mentions of How Music Works: The Science and Psychology of Beautiful Sounds, from Beethoven to the Beatles and Beyond

These are the 3 resources which kicked me into high gear:

• Music Theory From the Ground Up (youtube playlist)
  
• Scale Theory (Total of 3 youtube playlists)
  
• How Music Works (book).
  
  In my experience, these were the nuts-and-bolts foundational things I needed to start grasping theory.

I highly recommend this book, How Music Works, which covers this question in detail. Basically, a very, very long time ago, Western music starts with five notes. Then that scale was split further to create more interesting music, and then later on, standardized into what we have today. It could have been split indefinitely but that wouldn't have been practical, and further intervals would not have been significant enough to justify the split.

Each note/pitch/frequency in this scale has a mathematical relationship to one another. Some of the notes have more harmonics in common with each other, and therefore sound "stronger" together. Keys that are right next to each other, or semitones, have less overlapping harmonics than keys that are separated by a full tone, and so the relationship sounds "weaker".

Hope this helps. The book above does a much better job of explaining it.