Since the inner workings of the nether track are a mystery for most of the players I thought I'd try to explain how it's supposed to work.
Observe: a (not so) beautiful chart! [Only admins are allowed to see this image]
Firstly the track is meant to be one-way-only. This is because not too many players would use it to go from the end back to the hub. You can still ride it any direction you want; Be warned! The old Newtown stop will try to kill you if you approach it from the wrong direction!
To get a minecart at the Hub Station just press The Magical Button! This will dispense you a minecart on the track if any are available; If a cart doesn't magically appear on the track then cross your fingers and hope you stored one in your ender chest.
To leave the station simply hop into the minecart and press The Magical Button again and away you go!
After riding the long tunnel and a fall thru the nether your cart will be automatically recycled at the End Station. Basically a cactus breaks your cart pushing you off to the side and the minecart is sucked into a hopper.
BAM! You're at the End (Nether) Portal; But I hear you wonder: "Where did my precious cart go to?"
Well after being broken by a cute cactus it was sucked into a storage minecart. Once this storage cart is full it'll be sent back to the Hub station via a fancy sounding auxiliary rail. If all went well and the storage cart reaches the Hub station it'll be emptied to a holding chest by an unloader circuit. Your cart will wait in the holding chest until some other bloke comes along and wants to have a ride in the nether track. And the cycle begins all over again.
- - - - - - - - - - - - - - - - serious H4:
I know the nether track is almost always out of carts. This is because for some odd reason the storage minecart never reaches the hub station. I think this might be due to the fact that the tunnel is being loaded and unloaded all the time so the storage cart only moves 50 or so blocks when someone rides the tunnel to the end (since it's moving to the opposite direction).