Aside from the gender issue, I think a lot of Trek fans are preoccupied with captaincy as if it were the sole and universal career goal of everyone in Starfleet (and, apparently, even civilians like Guinan and Leeta!). In reality, the number of captains in any fleet is going to be finite, and there are plenty of other career paths besides ship command. After all, a captain couldn't do anything without officers in other jobs. The majority of people in a real-life navy will go through their entire careers without commanding a ship, and the same would logically be true of Starfleet as well.
True, most Trek series are ship-based and so you'd expect captains to be the main characters, but we have seen exceptions in the literature. We've had a book whose main character was the Federation president, one where the main characters were a pair of temporal investigators, at least one centered on an intelligence agent, and so on. In Vanguard
, the main character of the first few novels was a commodore, but for most of the series I don't think you could single anyone out as the main character, certainly not any of the starship captains.