Erm, the FS2 code is not built for flying inside large ships, since there's no type of face-removal except backface culling and frustum clipping. There's no PVS (a la quake) or portal-based stuff (a la UT, Descent Series), so basically you draw so much stuff you can't see so it can bog down even the fastest system (They didn't do all those portal-based renderers and PVS stuff for nothing, y'know). A pure Z-buffered implementation just won't cut it for anyone without a super system.
Edit: For the non-technical, what it means is that you're basically trying to draw everything, even when most of it won't be seen on-screen,making the amount of wasted pixels is huge, so either frame-rates are bad, or graphics are bad. Pick one.