Why are blocks often well below capacity?

[rbruggem]

See https://blockchain.info/charts/avg-block-size

[Emoclaw]

You should keep in mind that this is the average block size per day. This isn't a per-block chart.
With that said, the obvious answer is that there sometimes aren't many (big) transactions that fill the block.
Clicking 180 days shows that the blocks were constantly full amid the full-heat of the scaling debate (tons of spam attacks) until SegWit2X was announced.