Because commercial pilots are in control of aircraft flying over densely populated areas, and often responsible for the lives of hundreds on board. A navy pilot typically just has the expensive aircraft and is somewhat expected to be crazy.

So, if a commercial pilot does see such things, they'd be far less likely to report them, as it may well ruin their career. Navy pilots, on the other hand may well get some commendation for identifying an unusual, or anomalous thing (enemy tech?).