Looks cool, but have you considered making the tanks separate models? We have multidocking, and multiple-container ships are really friggen cool IMO. Plus, separate models mean the potential for separate textures, and multiple colours on the same ship.
Alternately, definitely at least make them destroyable submodels.
As for the rest of the model, three suggestions - take them or ignore them as you see fit. 
1. If you haven't already (I can't tell) flip it so that the bridge is underslung, like a zeppelin. No good reason, it'd just be cool and different, and since there's no horizon, there's no inherent advantage to being high up as opposed to down low in space - on either side, you're going to miss out on seeing fifty percent of the universe just because of the shape of the model.
2. Beef up your engines - you're making a freighter, which has to move a lot of weight. The engines look a tad puny right now.
3. That notch at the front is crying out for some kind of detail. I put a little secondary bridge up the front when I did my Atlantis (see the link above) and something like that might be appropriate here, or any other kind of doodad, but at the moment it looks kind of unfinished.
My 2c anyway. The fact that you're making civilian stuff at all is awesome. Good luck!
[EDIT]FWIW, I'm a big fan of unarmed civilian ships too. 
Good suggestions.
1. Feels awkward to me. Maybe with a more chaotic shape it might work better.
2. Agree to a certain extent, side engines will be going through an overhaul at some point but the main ones will most likely not be changed. I'll consider swaping the two thrusters into a really big one and see how it looks, low on my priorities though. I'm pretty happy with that part of the ship.
3. Putting it plainly that part looks like ****, mainly because of a total lack of inspiration for it. The secondary bridge was a pretty genious idea on that model you linked, It has changed my perspective on how that section could look.
edit: forgot to address the submodel feedback.
They were originally separate objects but I'm not sure how to justify that this huge container of (most likely) combustible material would not blow up the entire ship and anything near it if destroyed. If someone is escorting this vessel and fails he ends up paying the ultimate price.
On the other hand if someone wanted to use the model for say... transporting water its not too hard to detach those verts and play around with some supports for the tanks but fuel has been my idea from the start.