When you have rail or powered rail encased in a tube made of glass underwater, the track is invisible from above the water. See the screenshots. The wood and redstone is actually a trackbed. The second screenshot shows the view from within the tube.

HOW TO RECREATE:
1. Find a body of water
2. Make a completely enclosed tube of glass with a floor that rails can be place on.
NOTE: The glass tube needs to be COMPLETELY underwater or this glitch won't work.
4. Sponge out the water.
3. Place rails or powered rails on the trackbed
4. Fly over the glass tube
5. The rails will not be visible.

UPDATE:
If you are flying over the water and the trackbed is invisible, but a minecart is going on the track,
the minecart will be visible but not he track.