The system does produce a lot of military-background characters; it's partly a setting thematic (they're more likely to be the adventurous type, and to have some relevant experience and connections) and partly a legacy issue - the earliest edition only offered military careers; later editions added civilian options.
That careers like Navy and Scouts give great skillsets for operating a starship certainly doesn't discourage them.
It'll depend somewhat on the campaign though. General "adventures in space" scenarios are going to favor action-oriented characters; scenarios oriented toward diplomacy, intrigue, and investigation are more likely to put civilian skillsets center stage.
Of the three play-by-posts I'm in right now, the small one is civilian oriented (Scout, Noble, Scientist) and the two larger ones have mainly military/quasi-military rosters. (Although one of those is running Pirates of Drinax, which encourages rough and ready types.)