Actually, it's a bit odd that so few characters I've heard described doesn't have their families on the ship, now that I think about it.
That's a really good point, for the main officers and such anyhow (ie: most PCs). Clearly many of the workers on the ship would likely live there with their families, so why not them?
I actually wouldn't sweat too much about the whole "travel is boring" thing. An RPG is supposed to be fraught with peril and tension. I'd rather just skip through 95% of the travel if nothing happens so I can get to the action! We prefer to focus on travel when things DO happen. I think for the most part it's enough to just say: "After 3 months of mind-numbing boredom, eating bland dehydrated rations, you finally emerge from the warp near Planet X."
What has worked wonders for us is that we use the long travel times to deal with ship politics and personal business the PCs want to take care of: small mutinies, saboteurs, crime sprees, interrogating prisonners, planning expansion strategy, etc. After two or three sessions where this is all the business which is addressed, PCs will start to get a sense of the claustrophobic and repetitive nature of the long trips through the warp. (Maybe have them go to a bunch of meetings, do maintenance, etc. But too much of this will make the game boring instead of just transmitting to the players that warp travel can be boring.)
One of the strenghts of the Rogue Trader game is that, unlike most RPGs, your base travels with you. That means that you always have access to your contacts, networks, ressources, whatever. For instance, my navigator's sort of considered the Godfather of our ship, the Wrath of Icarus. A lot of crime goes through him. I've had so much fun playing this character specifically because he's almost always in touch with his power base: he's eliminating rivals, making new contacts, acquiring new loot. In some ways, our 'travel' sessions are some of the most interesting becasue it's during those times that we really develop our characters.