FOV is the main thing, but it also doesn't help that nothing in Freespace is really scaled to what it's supposed to be.
Valkyrie has a house-sized cockpit, as do many other fighters. Pegasus is probably the only ship with a cockpit similar in size to those on modern fighter jets. (Special mention also to Centaur, Ares)
Door on the Hermes is lol
Cutscene with elysium marine dump into the Cain (FS1) is probably wrong, though you could argue that the port they use is not the same one on the exterior of the transport (Marines compared to docking port)
Cargo container texture and model complexity makes the look like they could be people-sized, when they are actually office building size.
Windows on any destroyer. They're either ceiling-to-floor or span multiple floors. Except, they look as if they're supposed to be view ports half the height of a human.
A lot of destroyers suffer from lack of surface detail. Lots of ships look huge because of hull greeble to help give scale (eg, star wars destroyers). The orion (and even worse, the retail colossus) sport entire hectares of uninterrupted flat tiled hull. The tile texture also lacks tiny elements, so that doesn't help much.
The one time I remember that they get scale right is when they show the dead pilot beside his herc in the FS2 intro.