A number of people have suggested that Command or Tactical/Security get their own color to distinguish them from each other. In addition to red and white, purple seemed to be a popular choice for Command personnel in a Star Trek MMORPG as it would allow Tac/Sec personnel to once again be "redshirts." It was even noted that purple was historically associated with high rank of nobility.
That's true. "Tyrian purple" from the Murex snail was the specific color (called "imperial purple") used for Classical-era potentates, while a bluer purple ("royal purple") was used later by Western royalty.
But what I find most interesting about this is that purple is still used today to signify a specific high rank. Bishops in the Roman Catholic Church, unless they have also been named as cardinals or Pope, wear a purple "zucchetto" (skullcap) or biretta and purple vestments during ceremonies such as a Pontifical Mass. A bishop will also have a "pontifical ring" (in addition to his everyday episcopal ring) which is usually adorned with an amethyst stone for its purple color. (Cardinals, FWIW, are given pontifical rings by the Pope with sapphires mounted in them.)
(Side note: purple vestments are worn during Lent and Advent by regular priests as well as bishops, but as noted above there are several articles of attire and gear that are colored differently and specifically to distinguish one "rank" of the Roman Catholic hierarchy from another. Worn for certain ceremonies at any time of the liturgical year, bishops wear purple; cardinals wear red, and the Pope wears white.)
Of course by all this I'm not suggesting that a Star Trek MMORPG should adopt the color hierarchies found in Catholicism. (Although that could be interesting!) I'm just observing that purple is still used to signify high rank today, thousands of years after its first use. It wouldn't be at all surprising for that to be retained in some way even into the 25th century, even if many of the religious aspects have been shed.
Actually, it's interesting that purple, red, and white keep coming up as the colors of choice for high rank in Starfleet, isn’t it?
Perhaps millenia of associating these three colors with high rank are so hard to set aside that we just can't resist thinking of them as appropriate for top officers in Starfleet as well....