Captains are in charge of a company because that's their job -things like overseeing training, making sure all the gear is up to spec, as well as actual combnat leadership and tactical planning.* Librarians, as the name suggests, work in the Librarium. When they're not zapping Orks with their brain, they're in charge of long-range communication (and long-term strategic an operational planning in conjunction with the Chapter Master, I think). They don't have the time to also be in command of a Chapter.
Yes, Company Captains also have their other roles (Master of the Fleet, Master of Victuals, etc), but other than the 10th Company Captain, those seem more like sinecures. The Captain has to sign off on things, but all the actual work is done by non-combatant servants.
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