Starship Comparison Chart explains why some ships seem smaller.
If you have ever played our version of Star Trek Full Thrust (or Babylon 5 or Star Wars starship games) you will realise that there are two major issues, firstly getting models of the relevant ships and secondly getting ships which are in scale to each other.
The latter point is more difficult as often the ships would be of vastly different sizes to begin with.
A nice series of comparison charts can be found on this website.
As you will see some ships are really tiny, really tiny.