I have stayed at the cabins and we really like them. We are planning our next trip to stay there.
The transportation is only an issue if you make it one. For me, it's a whole lot easier and less time consuming than, for instance, going from my room at Boardwalk Villas on the bus to MK. The distance to walk to the bus stop at BWV is further than the bus ride to the Settlement! (okay a little exagerration, I know). At BW you have to get on a bus, stop at the Swan, stop at the Dolphin then finally to to MK. At the Fort, I have to get on a bus with a couple quick stops, then walk to the marina for the boat to MK, which is about the same distance as you'd walk from a room at All-Star Music in Jazz or beyond to the bus.
Something I didn't think of during our last stay in a cabin - yes, there's only one sink in the bathroom but guess what, there's one in the kitchen too! We never thought of using that one for face washing, tooth brushing, etc. Same thing for storage. There's a TON of cabinets in the kitchen and you likely won't fill them with food, so there's lots of storage.
If you have different age kids, the Fort really gives the older ones something to do while the little ones nap, or rest in the room. Being able to put the young ones down and close the door, while the older ones and adults can sit in the living room or on the deck is wonderful. Or go to the pool, or canoeing, or cane pole fishing, or bike riding, or swimming, or shuffleboard, or tether ball on the beach, or mouse boat rentals, or....

Plus you won't hear a single door slam or toilet flush from anyone else's room!
From the marina, you can take a boat to MK or a smaller boat to the Contemporary and Wilderness Lodge. From the Contemporary, you can hop the monorail and go to Epcot. Staying at the Fort is so relaxing, you can take your time and enjoy the different transportation options from there.
Maybe your TA thinks a vacation should be more luxury than a cabin in the woods. We'd rather spread out, relax and enjoy our time together, rather than squishing on the edge of a bed and step over each other to get to the bathroom.