Royal was trying color used when BYU made a brand for itself. Around 20 years ago someone in marketing decided that people were more willing to buy navy gear and the color was switched (starting with the horrendous navy/tan combos).
This was a deviation from the distinct BYU brand in an attempt to create a new one. Eventually (and after much pleading from fans and players, particularly legacy players) Royal was re-introduced for a few special occasions.
Players and fans that were around for the "glory years" view Royal as the BYU brand. Navy was a passing fad but is not the BYU brand.