Well, the color breakdown in the game is different than in the shows.
In the shows/movies (post TOS):
Red - Command. If your job is to order people around, you wear red.
Gold - Ship's Operations. Engineers, security, anybody who's job it is to keep the ship running wears gold.
Blue - Sciences. Doctors, chemists, astrophysists, if you do research, you wear blue.
While you'd get people like Beverly Crusher doing time on the bridge, sitting in the big chair wasn't her primary role, so she wore her standard Blues. Geordi started out as a bridge officer (command) in reds before being promoted to chief engineer, when he swapped out for gold.
Personally, my character is an engineer, but I still think captains should be in red. So, he has a red uniform with a gold undershirt and engineering comm badge as a nod to his secondary role.
And, just because James T. Kirk always looked so darn dashing in his remarkable wraparound, I've decided to grant my captain a unique and distinctive green uniform variant! While my bridge officers wear the colors of their respective disciplines, the captain stands apart in the away team. I don't believe there was ever a rationale given for Kirk's green variant but if it's good enough for the captain of the Enterprise, it's good enough for me!