What makes some frame's headtubes longer than others? --> frame characteristics is what dictates how big or long the headtube will be. Somebody mentioned fork also. Now a days with compact frames you can have frames with the headtube in any length the manufacturer wants for example some treks or specialized have a headtube so long that "at least for me" makes no sense to even put road handlebars to them, better just go and put flat bars.

All depends of the frame you are taking about also, racing track and racing road frames are so different that you could have a difference up to 2 cms in the headtube, being the track one the one with the longest head tube. The crown fork is barely touching the wheels, since it does not use brakes it is useless to even have room for them. The other factor that the BB is higher in the track bike, adding that maybe to a .5 to 2 cms shorter frame the same frame size for a track bike could add 2 cms more in the headtube.

Now if we talk about chap ass bikes as the old varsities or colegiate treks that are still moving around, or cheap asian stuff i would say that there is no rule, those bikes geometry is really weird so sometimes u have a 53 with a super short head tube and a 55 with a heaadtube so big that looks like a 60cm frame.

But basically that;s it, there are more details but why go onto them.