It's a little bit of everything, and an artefact of how BITRE collect/collected the data. In some cases it just counts some ad hoc flights including charters, while others were multi-stop flights (e.g. LAX-SYD that originated in BOS). Significant cities in other included Seattle, Boston and Detroit, while more occasional or once-offs included Washington, Orlando, Oshkosh (yes!), San Diego, Miami, Las Vegas, Atlanta, Cleveland and Denver.
Out of curiosity, what is the "other" US city listed in this chart between about 1998–2012?
It's a little bit of everything, and an artefact of how BITRE collect/collected the data. In some cases it just counts some ad hoc flights including charters, while others were multi-stop flights (e.g. LAX-SYD that originated in BOS). Significant cities in other included Seattle, Boston and Detroit, while more occasional or once-offs included Washington, Orlando, Oshkosh (yes!), San Diego, Miami, Las Vegas, Atlanta, Cleveland and Denver.