Not knowing your tech level and hardness of your science, this may not work, but...
Once we've become more commonly interplanetary/star-faring, it's likely that spaceships will be built in space or in gravity-light zones, and for practical purposes be designed primarily or exclusively for space travel. Spaceships don't need to worry about aerodynamics, collapse from outside pressures, etc. Could very well be that large blocky spaceships are more practical for jaunts in space, but due to weight, shape, and "uni-tasker" design are simply not suitable for travel through an atmosphere. Heavily armored to defend against the rigors of hard radiation, a pressureless vacuum, and space battles, these ships are just big lead weights. Could they land? Sure - if you had enough fuel to lower it slowly against gravity and to minimize atmospheric effects, and then to take off again, assuming that was even possible. On the other end, it could also be that these craft are built of light-weight materials to minimize fuel needs, and use some high-tech radiation shielding, and therefore be sort of "flimsy" compared to standard aircraft. Imagine the International Space Station trying to land.
If your tech is more of the "magical" sort like Star T/W/r/a/e/r/k/s, it's harder to reasonably justify not landing the big craft short of politics, military concern, or more magic. Like, landing a craft bigger than X breaks a treaty, is against an accord, looks suspicious, can't be hidden from enemies, etc. From a magical physics angle, maybe the "star drive" used to fly the thing doesn't work in a significant gravity well or atmosphere, thus it has to rely on chemical fuels and you're back to it being too heavy or such. Dunno.