idea for how they were able to fly a space ship..
so this is a really "lay-man's" idea for a probable explanation to the apes shuttling back to earth. it's quite rough but just an idea.
in the 1st movie, the ship with taylor and co. crosses a worm-hole and crash lands on a future earth.
this creates a tear in the space-time continuum. this weakens it, so that a similar occurrence is more likely (occurrence= a ship landing on this planet at this time(in the movie))
in the 2nd movie, let's consider that milo has been working on the ship and let's assume he's restored some functionality. how? i don't know. but its flux capacitor is lit.
the ship, built for light speed, has some sort of connection with time travel. the two are interrelated. the ship partially on is weakening the space-t.c.
at the end of the 2nd movie the detonation of the omega bomb, being that it isn't just a nuke, the power and energy from that is so great it creates a black hole/worm-hole and the ship passes through it arriving at earth for the 3rd film.
not a great explanation, but i'm still trying to think it through myself. i know it has holes galore, but there is just no way the apes could get the ship running, get fuel, and launch in any conventional way.
edit: or possibly the bombs energy is able to utilize the ships warp, or light speed drive and send the ship through a wormhole in the weakened space-t.c.